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1. cssccececeeecccceeceeseesesseeeesseeeeeeeeess 1 22 5 WP date tne PACA Ge Teen een rnit 1 228 Update LING SVS Ue messen ne beslontoess 1 229 Jnstallallon ol apache ennoun e eronmentadeueaseestnctetece 1 2 2 10 Ins Mau On On NS ee een es 1 2 2 11 Installation of maAllx and POS CE x rennen 12 2 2 12 Installation Orntpdale un en ana 12 2243 maybe required set a password for the Mysql root user cc ceseesseeeeseeeeeeecceeeeeeeeeeaeseeeeeeeeeees 12 2 2 14 Install some pack ases neccessary TOF CPAN Ga en 12 2245 optional Create a directory for the mysql binary logs 00000000 22 eeeeeeeeeeenneeeennnn 12 2 2 16 optional Comore MySQL Ta euer 13 22 17 COT ore CPAN seele avers dees 14 2 2 18 Installation of additional packages and Perl modules 0 00 cccccsssseeeeeeeeeeeeceeeeeeeeeeaaaaeeeeeees 14 2 2 19 Installation of packages required for statistics and Visualisation ccsseseeceeeeeeeeeeeeeeeeeeeeeees 15 2 2 20 Install xvfb Virtual Framebuffer fake X Server cccccccecccccesscccceseccceeececeusecsceeeceseeeeceeeueeseeees 16 2221 Synchronizesthe system ume to a ME SCHVER arer e A AE N 16 22 22 Switch off log flushing by the Ubuntu log rotate Service ccceecseeeeeeeceeceeceeeeaesseesesseeeeeeeeeees 16 2 3 InstallationOF Maus DB u 22a is 17 2 3 1 Download MausDB installation files ee ecceccceecccececceeceecaaseeeseeeeeeccceeeeeeeeeaaaaesaeseseeeeeeeee
2. EIPIBISIE BIGIAAE m p 5 ER CH What do you want to do with mice selected above genotype add change experiment add change cost centre order phenotyping view phenotyping data upload and link file to selected mice 1 M selectrandom subset Page generated on Tue May 15 15 09 56 2007 Figure 64 Mouse selection In the cart mice are selected using the checkboxes Pressing genotype in the bottom functions bar will lead to the genotyping procedure Logged in as admin log out Help MausDB DEMO u Y View mouse 3 mice in cart Home racks amp cages search amp find import reports settings empty cart Enter genotype phenotype information 1 step 1 Please choose the genetic marker to which genotype phenotype information refers defaults to genetic marker defined by mouse line Genetic marker abc J please check genetic marker 2a Either choose genotype phenotype that applies for all mice Genotype or phenotype for all mice ignore v this will be used for all mice unless left on ignore 2b or enter genotype phenotype information for mice listed below individually mouse id lear sex cage genotype phenotype 50005155 ss f 0296 w confirm genotypes cancel genotypin o to previous page Fage generated on Tue May 15 15 12 08 2007 Figure 65 Step 1 Genotype assignment In the first step the locus genetic marker t
3. aol as ee TEE What do you want to do with mice selected above add change experiment add change cost centre Page generated on Tue May 8 11 47 24 2007 Figure 24 Litter view The top box shows litter details for example date of birth date of weaning and comment The parents table shows parent mice of the current litter The bottom table lists all littermates of the current mating after mouse ID indicates that a mouse has been partner in a mating itself Parents as well as littermates can be selected and either put in the cart or used for actions that are made available by function buttons on the very bottom 38 4 7 6 Import view As every import defines an individual batch of mice the import view shows all information about an import How to set up an import in MausDB 1s described step by step in chapter 5 5 Logged in as admin log out Help MausDB DEMO W View mouse 0 mice in cart Home racks amp cages search amp find import reports settings Import details previous next Import 57 details Import number 57 Importname Strain Line C3HeB Fel Project Projekt_i Import type regular Date of import 06 12 2006 Import purpose purpose Owner no owners defined Provider name Charles River Provider Import by monika Healthreports no health report available no import comment Import comment update import comment Mice mouse
4. Upload from Excel file You can find a sample Excel file here D Documents and Settings holger maier My Documents import_template xls OR b use form to import mice manually O l import 0 males and 0 4 females or go back Figure 58 Step 1 Defining import details Top Box In the first row the date of import needs to be given In most cases import type should be regular Mice can be imported as external mice if they need to be managed by MausDB e g for data completeness or family relationship preservation but do live in rooms racks that are outside the facility which is managed by MausDB Important external mice are not taken into account when calculating mouse days see 4 13 6 or in the TEP report see 4 13 3 Strain genetic background and line can be choosen from a pulldown menu Alternatively new ones can be defined by selecting new strain or new line from the pulldown menu In the fifth line it must be stated whether imported mice are genetically modified or not Project and cost centre assigment are followed by the input field for the mouse provider All other fields in the top box are optionally There are two ways to import mice a import of batch mouse data from a spreadsheet file or b manual input of mouse data recommended only for lt 5 mice When using import from spreadsheet file a template file must be used available as link Pressing next step will lead to step 2 6
5. importing mice from external sources mouse breeding o mating o embryo transfer weaning moving mice cage and or rack transfers cage card printing locating mice full rack and cage overview collecting and grouping mice in so called carts or cohorts for statistical purposes genotyping mice multiple genotypes possible culling mice manage experiment licenses manage cost center assignment multiple cost centers possible breeding statistics per line sex ratio litter per mother average litter size mouse phenotyping o definition of structured phenotyping workflows o definition of phenotyping parameters o definition of phenotyping parameter sets parameters from one assay o schedule phenotyping tasks for single mice or groups of mice on a weekly basis query and manage status of phenotyping tasks o upload phenotyping results to database from spreadsheet files o extract and export phenotyping results from database to spreadsheet format o Statistical analysis and visualisation of phenotype data using pre defined R scripts via the MausDB web interface export mouse breeding data to spreadsheet files uploading and attaching custom files to single mice or groups of mice e g image files or spreadsheet files http www r project org 1 4 License MausDB has been made available under the terms of the GNU General Public License GPL See http www gnu org licenses gpl html for more details MausDB a laboratory
6. search amp find import reports settings New mating trying to set up new mating in the database Checking mating partners e checking male mouse 50005140 for mating ok e checking female mouse 50005146 for mating ok Moving mice moved mouse 50005140 from cage 0156 to cage 0240 e moved mouse 50005146 from cage 0225 to cage 0240 Setting up new mating Mating successfully set up in cage 0240 print cage card See mating 493 for details Page generated on Thu May 10 16 53 14 2007 Figure 44 Step 3 Confirmation Clickable links for mating ID and mating cage are displayed 5 2 How to set up an embryo transfer In MausDB an embryo transfer essentially 1s a special case of a mating In a normal mating both mating partners are already managed by MausDB and thus have a mouse ID In an embryo transfer the real mating event may have taken place even long time ago outside the facility that is managed by MausDB if frozen embryos are used The MausDB embryo transfer procedure records the event of implanting an embryo of whatever origin to a recipient female mouse As soon as this is done an equivalent to a normal mating is defined and subsequently litters can be reported and weaned Embryo transfers only can be started from the cart Another difference to setting up a normal mating is that the biological father can be optionally defined if available as a MausDB mouse or left out if it is an external mouse The recipi
7. 13 1 Mouse lines overview In order to get an overview about all mouse lines in MausDB choose reports line overview Mouse lines overview 76 mouse lines found Browse pages first previous nest last alive click on numbers to generate Excel report line name short line name long males females total al me rn ABC 129 saa l m am m a ABC B con ABC CON 26 23 4 aBe c coN ABC C CON ol ol 5 ABC C3H ABC C3H 34 42 6 ABC CON ABC CON ol ol 7 ABC FLP coN ABC FLP coN 41 3g e apc Gagoc ABC G640C 36 50 9 28C G640CxABC C3H ABC Gh40CxABC C3H ol al 10 ABexBCcD 129 ABCxBCD i29 ol ol 11 ABE C3H ABE C3H 22 35 12 BcDxaABC 129 BCDxABC i29 a ol ia C3HeB FeJ C3HeB FeJ 23 25 14 CS7BL 6 CS7BL 6 El 18 15 ELP B6 FLP B6 El 10 16 Foster Foster ol ol 17 SHI B GHI B ol ol 18 GHI B6 GHI B6 47 31 jis HIJ A B6 HIJ A B6 10 13 enl HIJ B B6 HIJ B B6 17 23 21 HIJ C B6 HIJ C B6 5 al 22 HU DEF ABC 129 HI DEF ABC 129 45 sill 23 HI DEF b6 HI DEF B6 al al 24 KLM CKO KLM CKO il ol 25 KLM KO KLM KO 5 2 Figure 35 Mouse lines overview All mouse lines are listed alphabetically Multiple result pages can be browsed using the navigation links on top of the table Clickable line names lead to line specific detail views Clickable numbers show current live stock of male female
8. 13 18 2007 Figure 10 User specific Home area with examples Six litters assigned to the user s project have been reported to MausDB Litters that are ready to wean i e 21 days or older are displayed in red Clicking the link in the leftmost column directly leads to the weaning dialog Two tasks have been scheduled for the user The tasks are ordered by their scheduled week Clicking the link directly leads to the task list where the task list can be viewed or modified 4 2 3 Changing the password The password can be changed at any time via settings change password The password should be changed during the first MausDB session or after an administrator set a new password respectively In either case the previous password must be entered before entering the new password twice After changing the password a login is enforced Logged in as admin log Help out MausDB DEMO i Y View mouse Cy Home racks amp cages search amp find import reports settings 0 mice in cart Change password Please enter old password and new password twice old password new password repeat new password Warning pressing the lt changing password gt button will terminate the current session You will have to log in again using your new password change password cancel Page generated on Mon Apr 30 13 27 11 2007 Figure 11 The Change password screen 29 4 3 The Quickfinder tool find mice and
9. CS7BL 6 BTNT KLM KO Projekt_ 2 0 mating 48 26 03 2007 SERS BTNT KLM KO Projekt_ 2 0 matin 434 23 03 2007 ABC FLP con Projekt_ 2 0 matin 48 23 03 2007 ABC FLP CON Projekt_ 2 0 matin 48 23 03 2007 ABC FLP CON Projekt_ 2 0 matin 48 23 03 2007 ABC FLP CON Projekt_ 2 0 matin 48 23 03 2007 ABC FLP CON F4 Projekt_2 0 matin 47 23 03 2007 aBc FLP CON FS Projekt_2 0 matin 47 23 03 2007 ABC B CON F6 Projekt_2 0 matin 47 23 03 2007 ABC B CON dey Projekt_2 0 matin 47 23 03 2007 ABC B CON F6 Projekt_2 0 mating 474 23 03 2007 aBc B con Projekt_2 0 mating 47 23 03 2007 ABC B CON Projekt_ 2 0 matin 47 23 03 2007 ABC B CON Projekt_ 2 0 matin 47 23 03 2007 ABC B CON Projekt_ 2 0 matin 47 23 03 2007 ABC B CON Projekt_ 2 0 matin 46 23 03 2007 ABC B CON Projekt_ 2 0 mating 46 23 03 2007 ABC B CON Projekt_ 2 0 HN N Il nn NN SREIREIEISIEISIEIEIE err 5 co Figure 27 Mating overview All matings are shown by default and multiple result pages can be browsed using the first most recent previous next and last links Matings can be
10. Commented SQL scripts for some frequently used tasks are available from the downloaded repository and should be located in home admin mausdb SOL WARNING MANIPULATION ON DATABASE LEVEL IS PRONE TO GENERATE DATA LOSS OR DATA CORRUPTION PLEASE NOTE OUR ADVICES ON SQL LEVEL DATABASE MANIPULATION 1 Make a full database dump before manipulating the database 2 set a global lock before manipulating the database see 6 2 3 read the commented scripts carefully before running them 4 make sure you fully understand what the scripts are doing before running them 5 in case you feel unsure about 4 ask someone with more SQL skills for help 6 Think twice before executing SQL commands 7 for update commands make sure there is a where clause in your statement 8 for delete commands make sure you also delete corresponding entries n other tables in order to maintain referential integrity 72
11. be chosen The number of mouse days will be calculated within short time 48 Logged in as admin Help log out MausDB DEMO 0 5 a Home racks amp cages search amp find import reports settings mice in ca Animal cage occupation in area Floor_A Total number of mouse days from 01 04 2007 to 30 04 2007 in area Floor_A Cost centre MausDB_account_1 Experiment GYO Inon Gvo sum GYO non GVO breeding 16214 6540 ee fot total 16214 6540 ee fod Page generated on Wed May 9 11 00 48 2007 Figure 41 Result of cage occupation calculation For a given time period and area mouse days are calculated Numbers are calculated separately for genetically modified GVO and genetically non modified mice non GVO 49 5 Detailed step by step instructions for common tasks 5 1 How to set up a mating The origin concept of mice in MausDB strictly requires a mating to happen before offspring can be weaned It is important to stress that in MausDB a mating is defined on an abstract level as the possibility that one male mouse and at least one female mouse can mate and produce offspring As soon as such a mating is defined litter can be reported and weaned Litter reporting is a precondition for weaning Important The mating is not at all coupled to co caging during a mating the mating partners do not necessarily have to be housed in the same cage 1 e there is no automatic mating when males a
12. cages Using the quickfinder input window upper right corner of the MausDB user interface you can access details about a specific mouse or a cage very fast Just enter the 8 digit mouse ID or a cage ID into the form and press the View mouse cage button Alternatively you may place the cursor into the form and read a mouse ID or cage ID barcode with a barcode reader from a printed cage card In either case entering a valid mouse ID from an existing mouse will result in being forwarded to the mouse details or the cage view see 4 6 of this particular mouse cage 4 4 Locating mice browse racks amp cages Locating mice by browsing racks and cages 1s a straight forward approach since it does not require prior knowledge about mice such as line sex or genotype 4 4 1 Rack overview Choose racks amp cages from the main menu Logged in as admin log out Help MausDB DEMO Home racks amp cages search amp find import reports settings Rack overview or enter cage number s Search cage s Showing active racks show all racks show racks from your screen s only ann Cage summary total number total z of mice in project assignment comment shortened racks ETA in use free cage slots in use and free this rack 0000 Virtual rack 00 40 00 40 0 Projekt_1 virtual rack Floor_A rack 01 rack 02 40 17 23 HEKKAKAAKAAEAAAAT 40 Projekti 40 26 14 DEE 22 61 Pro
13. change to v change schedule date assigned to rey parameter set Sperm freeze status done no comments for this orderlist comment update comment Do you really want to delete all medical records uploaded for this orderlist elete orderlist data yes I want to delete all medical records from this orderlist delete uploaded data from this orderlist Parameterset specific metadata No parameterset specific metadata stored or even defined Mice on orderlist There are 9 mice on this orderlist view record stats edit status status codes Miera O A nerea e is O EEE U eme undefined y Figure 31 Orderlist view A list of 9 mice is scheduled for sperm freezing for a specific date In order to generate an orderlist or a series of orderlists start from the cart select your mice and choose order phenotyping In the next step either choose a user defined workflow or a previous defined workflow Order phenotyping 1 step Please specify phenotyping workflow mouse id fear sex go 22ssol24 m_ phenotyping next step Figure 32 Order phenotyping 1 step Choose a workflow for selected mice In the next step specify tasks parametersets and their corresponding due dates Finally confirm your order which will result in the generation of orderlists The orderlists will be displayed on the Home page of MausDB 4 11 Loading phenotype data into MausDB
14. count The number of animals housed in a given area at a given point in time can be determined using the snapshot tail count function Logged in as admin Help log out MausDB DEMO ae Home racks amp cages search amp find import reports settings 0 mice in cart Snapshot tail count Calculate animal numbers for any point in time Please define point in time 09 05 2007 10 57 07 E Please specify area FloorA generate animal numbers Page generated on Wed May 9 10 57 07 2007 Figure 39 Snapshot tail count A point in time and an area can be chosen The number of animals will be calculated within a few seconds 4 13 6 Cage occupation The number of mouse days n a given time period and area can be determined using the cape occupation function One mouse day is the equivalent of one mouse being housed one day and can be used for cost billing purposes for example Logged in as admin Help log out MausDB DEMO A view mouse an Home racks amp cages search tind import reports settings 0 mice in cart Animal cage occupation Calculate animal cage occupation for a time range Please define a start date a 04 2007 10 56 49 EJ Please define an end date 30 04 2007 10 58 49 EJ Please specify area Floor_A generate animal cage occupation Page generated on Wed May 9 10 58 49 2007 Figure 40 Cage occupation A time period and an area can
15. e g mysql_binlogs 12 e set correct rights for this directory sudo chown mysql adm mysql_binlogs 2 2 16 optional Configure MySQL Configuration of mysql is done in the file etc mysql my cnf Before making changes to the configuration stop mysql t sudo etc init d mysgql stop Attention adapt the entry server id Every server needs its own ID Change to etc mysql cd etc mysal Make a backup copy of the config file teuda CO myn Men cold Edit etc mysql my cnf sudo nano etc mysql my cnf Add or change the following lines client default character set utf 8 add mysqld character set server utf8 add default collation utf8 unicode ci add init connect SET NAMES utf8 add server id 1 possibly change binlog do db mausdb possibly change log bin mysql_binlogs mysql bin log possibly change binlog ignore db mausdb_demo possibly change Choose binary logging for every MausDB database but not the blob databases After making changes to the configuration you need to restart mysql sudo CtC ini ead mysql start gt if you don t have to deal with special characters Umlaut accents you may skip this 13 2 2 17 Configure CPAN Using CPAN Perl modules can be easily downloaded and installed from the CPAN repository or its mirrors Prerequisites and dependencies are resolved automatically Short introduction to CPAN Start CPAN sud
16. filtered to show only active matings which means matings for which no end date is defined Clickable mating IDs lead to the detailed mating view of the individual mating 4 8 2 Import overview All imports ever defined in MausDB can be listed in the import overview Import overview quick find _ Search by import ID_ Found 59 imports new import Browse pages first previous next last e import numberlimport namelfice sera _ Une _ Timperttypelbste ef import Provider Jeroviderlongin Interosilimper ty TmportconmantTgbortenel i import 59 NOT1 G4 reqular 12 03 2007 Charles River no import comment 2 import 5 Foster reqular 29 01 2007 Charles River Tapers e ecane eer 90 0 2006 cheres river import 54 C5S7BL 6 regular 31 07 2006 Charles River neasa Maa aa eee a e mport 5 9 ee TE BEE STOSS BEE mport 4 ABC 129 regular 20 12 2005 Charles River mport 4 aa Sate wake mae ioe i no import comment mport 4 OO aS c57BL 63 regular 02 08 2005 Charles River i no import comment a a m E m a a N j on no import comment iw uo no import comment no import comment peN oa no import comment no import comment no import comment no import comment no import comment no import comment i no import comment i re un mport 4 Hm B
17. from this import O mouse ID lear SEH born death genotype strain line room rack cage ifm sooo4249 KB 19 09 2006 21 12 2006 C3HeEB Fel m s0004250 HA 12 03 2007 C3HeB Fel C3HeEB Fel c3Hep Fes z l C3HeEB Fel 21 12 2006 cm O sposs2s1 23 f 20 12 2006 0004252 has _ Add selected mice to cart What do you want to do with mice selected above genotype add change experiment add change cost centre order phenotyping Page generated on Tue Way 8 11 51 45 2007 Figure 25 Import details The top box shows import specific information The table lists all mice that belong to this import Mice can be selected and either put in the cart or used for actions that are made available by function buttons on the very bottom 39 4 8 Finding mice by properties the search amp find page In order to find mice not by their location 1 e rack and cage browsing but based on other properties the search amp find functions of MausDB can be used Search amp find Browse browse matings browse imports Find mice Optional restrict search to cart by mouse ID s a by cage ID s by date of birth by date of death Birth after 01 01 2006 Death after 01 01 2006 Birth before 01 02 2006 Death before 01 02 2006 search by mouse IDs Search cagel Search by date of birth Search by date of death by line sex a
18. lock should be set This prevents new data to be written to the database and facilitates database rollback and point in time recovery o when the database server needs to be stopped for service or updates 6 2 1 Setting a global lock via web user interface Log n using an account with admin rights and choose set or release global locks from the settings menu The web user interface for non admin accounts will immediately be blocked Be aware that the web interface for admin accounts will not be blocked and remains accessible As admin you will be able to work with MausDB and finally release the global lock again 71 6 2 2 Setting a global lock manually In case the web user interface is not accessible you may set a global lock manually 1 Open usr lib cgi bin mausdb config rc in an editor Sudo nano jusr lib cgi bin mausdby config re 2 set MAUSDB_LOCK from false to true 3 repair manipulate the database or run updates on your server 4 set MAUSDB_LOCK back to false 6 3 Administrational overviews and settings Users with administrative rights user_role ua can access many frequently needed administrative functions via reports and settings in the main navigation bar 6 4 Administration on database level However some infrequently needed or complex functions are not integrated into the web user interface In these cases database manipulation has to be carried out on database level
19. managed by MausDB must be imported in order to get mouse IDs The import procedure in MausDB includes the generation of mouse IDs for all imported mice eartag assignment and rack cage allocation of these mice In the following example a batch of 3 males is imported Import 1 step 1 Please enter some details for your import date of import 15 05 2007 14 23 17 EJ please check date of import import type regular extemal Oregular Oexterna external mice will not be taken into account for TEP reporting or cost please specify regular C external calculations strain strain that litter from this import will be CS57BL 6J BTNT optional for new strain only name of a assigned to strain line line that litter fror this import will be ABC 129 optional for new line only name of the new line assigned to are imported mice wi Sadia yes Ono please choose GVO status of imported mice s import for project your screens projects only or allscreens projects assign a screen project i which project will take care for the mice Projekt_1 hi Projekt_1 bs cost centre help i assign a cost centre Cost centre to bill mouse housing costs to MausDB_account_l Who will pay for the mouse housing costs provider Dr M ller Smith Berlin who sent you the mice optional owner s of intellectual property optional import name optional import comment 2 how do you want to import your mice a
20. of mating 494 entered left i amp parental O role mating En mouse ID jear sex born age death lsenotype strain line Iroom rack cage ats recipient ll ze E RA i O mother 11 05 2007 0003930 30 f 13 09 2006 240 y HIJ B B6 DO 0005 remove Add selected mice to cart Litters from mating 494 No litters found for mating 494 Details for mating mating 494 Mating type embryo transfer 6 Mating name ik Mating start 11 05 2007 Mating end Stop mating 11 05 2007 10 47 26 EI enter date time for mating end Strain C57BL 6J Line ABC B CON Mating scheme embryo transfer Mating purpose Mating generation assigned project Projekt_1 mating comment update mating comment Figure 48 Mating details view for an embryo transfer The first row of the second table Mating type contains a clickable link that leads to an embryo transfer specific view see below 54 Logged in as admin log out Help MausDB DEMO VW View mouse 2 mice in cart Home racks amp cages search amp find import reports settings empty cart Embryo transfer details Details for embryo transfer transfer 6 embryo transfer 6 mating id mating 494 embryo id TNFa 123 07 embryo origin embryo production lin_vitro IVF assistance none embryo preservation fresh sperm preservation fresh transgenic manipulation Ino_manipul
21. print card Add selected mice to cart What do you want to do with mice selected above add change experiment add change cost centre order phenotyping Figure 13 Rack details view In this view all cages of a chosen rack can be viewed showing one cage per row condensed view e g cage 0005 A click on the cage id in the first column leads to a detailed cage view Clicking the cage link will start a cage transfer dialog see 5 10 whereas clicking print card will open a cage card preview in a new window see 4 4 4 Cages can be expanded using the switch on the left hand side of the cage id in the first column expanded view e g cage 0012 Basic information of individual mice is displayed along with a clickable mouse ID which leads to a mouse details view see 4 6 Clicking the mouse link will start a mouse transfer dialog see 5 9 Mice can be selected across cages and be put in the cart see 4 5 by checking the box in the second column and pressing the Add selected mice to cart button Some actions can be applied on selected mice using the buttons in the bottom row e g kill see 5 11 mate see 5 1 genotype see 5 6 4 4 3 Cage view Following a link from the rack view or any other mouse table an individual cage with all mice can be displayed 31 Cage view or view another cage Search cage s Cage 0018 placed in rack 1001 01 Projekt_1 contains 2 mice print c
22. rack history of cage ID Current cage color MMM Change to blue update color e C mouse 1D ear sex born a lgenotype strain line room rack cage comment shortened move mouse O s0005138 3e 13 03 2007 SE HU 8 86 1001 01 0018 more mouse 2 O fso00si39 39 13 03 2007 HD B B6 1001 01 0018 move mouse Add selected mice to cart Figure 77 Starting a cage transfer to another rack from the cage view Clicking move cage on top of the color bar will start the move procedure for that cage Move cage Move cage 0018 from rack 1001 01 1 Move date 15 05 2007 16 39 11 E 2 Please choose target rack racks from your screen or all racks 1001 01 Projekt_1 28 free slots 7 move cage or cancel go to previous page Figure 78 Definition of move date and target rack Racks can be chosen from own project linked racks or from all racks managed by MausDB Pressing move cage will finalize the procedure Logged in as admin log out Help MausDB DEMO y view mouse 0 mice in cart Home racks amp cages search amp find import reports settings Move cage Moving cage 0018 from rack 1001 01 to rack 1001 04 at 15 05 2007 16 39 11 trying to move cage successful print new cage card Figure 79 Confirmation The cage transfer is confirmed and a clickable link to the cage card is displayed 69 5 11 How to cull mice As with other standard procedures cullin
23. the package repository apt cache search lt searchterm gt Get details about a package apt cache show lt packagename gt Update the package index sudo apt get update Upgrade the system will install up to date packages sudo apt get upgrade 10 2 2 5 maybe required de activate the installations CD as a package source In order to get the latest updates from the remote Ubuntu debian repositories etc apt sources list must be changed sudo nano etc apt sources list comment out the line starting with deb cdrom 2 2 6 may be required Including the universe package sources Some packages are only available using the universe package sources sudo nano etc apt sources list un comment activate the line starting with deb universe and deb src n verse 2 2 7 Update the package tree The package index file package tree must be updated in order to set up a system which s as safe as possible sudo apt get update 2 2 8 Update the system All packages that can be updated will be updated by typing sudo apt get upgrade 2 2 9 Installation of apache Install the apache web server by typing sudo apt get install apache2 2 2 10 Installation of mysql Install the mysql server by typing sudo apt get install mysql server You may be asked to give a password for the mysql root user during installation Please be aware that the mysql root account s different from the sys
24. var www mausdb static Content home admin mausdb code var www mausdb static_pages home admin mausdb code var www mausdb R home admin mausdb code var www mausdb R output home admin mausdb code usr home admin mausdb code usr lib hnome admin mausdb code usr lib cgi bin home admin mausdb code usr lib cgi bin mausdb home admam meme cio Code mer imib Cqu ban menmedio calles home admin mausdb code usr lib cgi bin mausdb logs home admin mausdb code usr lib cgi bin mausdb sessions home admin mausdb code usr lib cgi bin mausdb uploads home admin mausdb info home admin mausdb services 2 3 2 Settings based on a typical Ubuntu installation Assumption made for the following steps apache htdocs folder is located at var www apache cgi folder is located at usr lib egi bin connection parameters var maus_connect apache system user www data group www data 17 2 3 3 Install the MausDB script files Copy the directories and files from the above directories to their target directories var var www usr lib cgi bin and set ownerships to www data www data cd var sudo cp R home admin mausdb code var cd var www sudo cp R home admin mausdb code var www sudo chown R www data www data mausdb tcd Zusr rib cgi bpin sudo cp R home admin mausdb code usr lib cgi bin sudo chown R www data www data mausdb 2 3 4 Configuration of MausDB adapt connection parameter
25. week and TEP key genetically modified yes no breeding or experimental name TEP report Generale a TEP report Please choose the report period From 13 2007 to 19 2007 generate TEP report TEP Excel file will be produced upon pressing the button You can download the file to your local system or open it directly Page generated on Wed May 9 10 53 02 2007 Figure 37 TEP report The report time period must be selected on calendar week level An Excel file will be produced which can be imported into the Helmholtz Zentrum M nchen TEP system 4 13 4 Specific to Helmholtz Zentrum Munchen Versuchstiermeldung The Versuchstiermeldung German expression for laboratory animal report produces another set of statistical information For all months of a given year the number of animals which were newly assigned to a given experiment is calculated Yersuchstiermeldung monthly Generate a Versuchstiermeldung number of mice that started into experiment each month Choose experiment 234 47 w Choose year 2006 _ generate Versuchstiermeldung Page generated on Wed May 9 10 56 15 2007 Figure 38 Versuchstiermeldung For a given year the number of animals used every month in the course of a given experiment is calculated Helmholtz Zentrum M nchen German Research Center for Environmental Health Ingolst dter Landstr 1 D 85764 Neuherberg Germany 47 4 13 5 Snapshot tail
26. 1 ee el IE re RE a IM oe MOOR CATID earlag conlag stral DOB Pala Malad Mald 10153249 99 1401 193941 10135233 10139242 10153250 90 17 02 7996 10136239 10139242 10153448 D1 jl 23 01 1995 10142679 10142602 10153451 96 25 01 1996 10139227 10139231 1015345215 Bl 25 01 1996 10139227 10139231 10151554 16 H 30 12 1997 10144912 10144719 Figure 59 Spreadsheet template file Batch mouse data can be imported from a file Important column headers must be exactly as shown here Columns A mouse ID C cage ID E sex f m F date of birth dd mm yyyy G ID of father H ID of mother1 I ID of mother2 optional Logged in as admin log out Help MausDB DEMO y view mouse 0 mice in cart Home racks amp cages search amp find import reports settings Import 2 step Trying to upload Excel file file import_template xls successfully uploaded Using the first sheet of uploaded file import_template xls 14848 bytes which contains 3 rows of data Line MausDB ID external ID ear tag cage sex born father 1 mother 2 mother comment afto be assigned 10153249 69 new_1000 Om 17 01 1998 1013823 10138242 Fan 10153250 se new_1000 Om Of 17 02 1998 1013823 10138242 afto be assigned 10153448 fo1 _ new_1000 Om f 23 01 1998 1014267 10142682 or go back Page generated on Tue May 15 14 32 59 2007 Figure 60 Step 2 Data capture from Exce
27. 22 m 05 01 2007 126 1 aec rir con 100 2 C mother 50004625 25 Jos o2 2007 6 ie ac Fir con Pups not weaned yet click to weani or report litter loss What do you want to do with mice selected above add change experiment add change cost centre order phenotyping Page generated on Fri May 11 14 05 55 2007 Figure 53 Step 1 Starting the weaning dialog from the litter details view see 4 7 5 An already reported litter can be weaned by following the click to wean link on the bottom Alternatively if pubs are gone this can be reported by following the report litter loss link 57 Logged in as admin log out Help MausDB DEMO Y Wiewmouse 2 mice in cart Home racks amp cages search amp find import reports settings empty cart Weaning 1 step 1 step Please enter litter details for 1 litter from mating 489 line 4BC FLP CON strain date of birth 18 04 2007 14 03 00 gJ please check date of birth date of weaning 09 05 2007 09 00 00 EJ weaning type Bar mice will not be taken into account for TEP reporting or cost please specify O regular O external calculations Sati oe difi d yes default has been determined gene G Os me O no automatically by parent gvo status so please check cost centre help assign a cost centre who will pay for the mouse housing costs FP Eoo mes E femes Cost centre to bill
28. 4 y hijl F 50004725 25 mo S0003930 sooo 726 26 P 29 01 2007 NN 50803024 HIJ B B6 gt FSo004726 26 Mo 50003930 y hi M 12 o 80005924 U004 727 27 23 01 2007 I HIJ B B F 50004727 27 mo 50003930 y hiji _ Prm amp d Monday 7172009 2007 Figure 15 Cage card Left part in the top row room 1001 and rack 01 are denoted on the left the cage ID 0297 is printed on the right whereas the color bar is centred Mouse specific rows contain mouse ID eartag sex and date of birth in the first line Strain background and line information are printed on the second line Genotype information is given in the third line and comments on the fourth line Right part in the top row the cage ID is barcoded Mouse specific rows contain a barcode of the mouse ID together with sex mouse ID and eartag The origin of the mouse M mating weaning I import with the correspondent mating or import ID is given IDs of father and mother are printed below 32 4 5 Collecting and grouping mice the cart In MausDB the so called cart plays an important role for collecting and grouping mice Most functions can be carried out via a three step procedure some functions even require it e first step locate and identify a set of mice e second step select mice and put them into the cart e third step open the cart and apply a function on selected mice in the cart Putting mice in a cart is like writing a mouse ID on a piece of p
29. B6 regular 01 10 2005 Charles River no import comment import45 I Fir B6 regular 05 01 2006 Charles River re un EN re no import comment no import comment import 44 In C57BL 6J regular 15 03 2005 Charles River ABC CON regular 15 03 2005 Charles River C57BL 6J regular 14 01 2005 Charles River HIJ C B6 regular 14 02 2005 Charles River ABE C3H regular 01 02 2005 Charles River HIJ B B6 regular 14 06 2005 Charles River C3HeB Fel regular 01 04 2005 Charles River mport 3 a GHI B6 regular 04 12 2005 Charles River import 3 CS7BL 6 regular 01 07 2005 Charles River i no import comment 25 import 35 HIJ 4 B6 reqular 01 02 2006 Charles River i no import comment mport 4 a mport 4 er 7 mport 4 a mport 4 mport 3 We 1 mport 3 no import comment no import comment no import comment no import comment i no import comment no import comment no import comment FLEE EEE 5 6 7 87 o ho fat fiz 3 ha fas Imp 5 lie lt he fis 20 fet 22 23 lea l Figure 28 Import overview All imports are shown Multiple result pages can be browsed using the first previous next and last links Clickable import IDs lead to the detailed import view of the individual import 41 4 9 Managing your phenotyping data Parameterse
30. IDs can be entered Pressing next step will lead to step 2 58 Weaning 2 step 2 step assign eartags and weaning cages male pups choose racks for new male cages cage rack info E 1001 02 Projekt_1 12 free slots choose rack for all cages w_1 1001 02 P Projekt_ 1 12 free slots slots v or go back no female pups to wean update weaning preview or go back Figure 55 Step 2 Eartag and cage assignment The top table shows a preview for weaned mice Mouse IDs first column will be generated at weaning time eartags are incremented from the start tag given before or will be set according to the last two digits of the mouse ID at weaning time In case no cages were given to fill up with weaned litter cage IDs will be determined at weaning time so they cannot be displayed here Instead a temporary cage ID placeholder new_1 will be displayed This cage ID placeholder can be edited at this stage The placeholder can be anything but a number which would be interpreted as real cage ID Mice assigned to the same cage ID placeholder will be caged together The second table allows to assign cages to racks This can be done individually or for all cages first row Pressing update weaning preview will re check for errors and the availability of cages and racks and can be repeated again and again The screen is splitted for male and female pubs The update procedure affects both As so
31. MausDB Installation Guide And User Manual Holger Maier Version 1 5 March 2010 Helmholtz Zentrum M nchen German Resarch Center for Environmental Health GmbH Institute of Experimental Genetics Ingolstadter Landstr 1 D 85764 Neuherberg Germany 1 Content T UNERODUGTION ee seen ae ne tere nce east ee 6 1 1 Definition purpose and intended use 00000000uuuuuosssssssssssssssssssnnnsnnnnsssssssssssssssssssssssssnssnsssssssssnse 6 1 2 Technical Information a3u50en a beste cauccacocsanscoaceusedasucssostecoussavecsssnoveseanecssnssboosadeases 6 1 3 Maus DB Teatures an RE HARRIS eT ELLE UeE See 7 1 4 1 COMISC E NEN EEEE AEEA E OE EN EEE AEA 8 1 5 Belore usme MausDB nu ee 8 2 INSTALLATION see ae 9 2 1 I CIOL YOU Start a en crude cacsvecuvecdencecsceascvecsdsuseusexcaxsececeneesecctetsauudausieeacvencdeccececeescueecsusaassueceeccueteitase 9 2 2 Setting up a Linux system as MausDB server 0200000000000000000000000000000ssssnnnnnuunnnnssnnnssssssssssssssssssssssnnee 9 2 2 1 Standard installation of Ubuntu Linux 8 04 LTS server edition from CD cece ceeceeceeceeees 9 ALE RM SSS Gy A Te ee ee ee 10 22 SS ins LAW ATION see eehetesit a corte ca haneieamnes ee meets 10 224 SNOL MUMOGUCHON To Apsis 10 2 2 5 maybe required de activate the installations CD as a package source essssnsneeneeseeeeeeeeeeno 1 2 2 6 may be required Including the universe package sources
32. MausDB DEMO 0 mice in cart Home racks amp cages search amp find import reports settings Cage history of mouse 50004217 Mouse 50004217 was placed in the following cages in cage from to together with with cage being placed in rack _ esse rn 1002 16 from 29 11 2006 09 00 00 to 17 01 2007 11 01 21 0225 29 11 2006 09 00 00 25 01 2007 16 35 10 50004216 banisi ina eee iat 2007 T 2 D oa ony Tain So 1002 13 from 17 01 2007 10 44 04 to 14 02 2007 13 50 55 0010 25 01 2007 16 35 10 still there 50004147 50004517 1002 15 from 14 02 2007 13 50 55 to 22 03 2007 14 07 00 En a iz IL i 1002 16 from 22 03 2007 14 07 00 to cage still there Page generated on Tue May 8 10 27 00 2007 Figure 20 Cage history of a mouse The complete cage transfer history of a mouse is recorded and can be viewed for sanitary purposes for example The time range from to of cage allocation is given in a a row for every cage a mouse has been placed in the past up to present time Cagemates of the current mouse are given for the respective cage and time in the fourth column For every cage the rightmost column lists the rack allocation during the respective time range 35 4 7 2 Rack history of a cage Sometimes it is interesting to know in which racks a cage was placed in the past To be exact to which racks a cage ID was assigned in the past since cage IDs are being reused in MausDB and are not an attribute of a physi
33. One basic principle is not to disallow actions in MausDB that can be done in the real physical world but rather only display a warning Also managing grants to allow disallow actions kill move on a user project base makes no sense if there are no such mechanisms in the real world This works well in the German Mouse Clinic 21 4 2 Getting started 4 2 1 Logging in to MausDB In order to work with MausDB you need to login in to the application Point your Mozilla Firexfox browser to the appropriate URL given by your administrator e g http mausdbwww yourdomain cgi bin mausdb mausdb cgi Enter username and password for your account to get access to MausDB GSF Forschungszentrum f r Umwelt und Gesundheit t Helmholtz Gemeinschaft MausDB DEMO the mouse management system of the German Mouse Clinic 1 in de Welcome to MausDB Please log in user hame password Page generated on Mon Apr 30 13 24 48 2007 Figure 8 MausDB authentication screen login to specific user account is required 4 2 2 The Home area Following authentication a user specific Home view is displayed User and project specific information is displayed here Logged in as admin log out 3 Help MausDB DEMO i Y1 2 0 mice in cart Home racks amp cages search amp find import reports settings Welcome MausDB Admin Currently no litters to be weaned from your screen s Currently no order lists from y
34. Parametric phenotype data can be uploaded into MausDB using Excel sheets For every parameterset columns can be defined interactively via the web interface see above Once defined data can be uploaded from Excel files starting from a specific orderlist select mice 43 from orderlist then press button upload data for mice from this list In the next step the file has to be located on your file system and the the sheet can be chosen Upon upload mouse ids from the orderlist and from the specified column in the Excel file are matched An example Excel file home admin mausdb info example xls is available in the download repository In order to be able to use this example mice with corresponding mouse ids must exist in the database and be part of an example set orderlist You may also adjust mouse ids and dates of measurement in the Excel file columns A and B Upload phenotyping data 2 step Trying to upload Excel file file example xIs successfully uploaded Using sheet Sheet1 of uploaded file example xls Please use the checkboxes to select or de select rows mice and or columns values for dat 0 errors Please provide some additional data project to which data belongs lis data public yes Ono maier Holger Maier v maier Holger Maier v or go back Figure 33 Uploading phenotype data Data is matched via mouse id columns in orderlist and Excel file 4 12 Statistics and visualis
35. _1 contains 1 mouse mouse ID lear sex born age death genotype strain line room rack cage 1 50003330 30 f 13 09 2006 244 y Hn B B6 1001 01 0005 move mousel or cancel go to previous page Figure 75 View into an existing cage In case an existing cage has been chosen as target cage a view of current mice in this cage is displayed as a means of control Pressing move mouse will finalize the procedure Move mouse Moving mouse 50005155 from origin cage cage 0296 in origin rack rack 1001 01 to target cage cage 0005 in target rack rack 1001 01 trying to move mouse successful print new cage card Page generated on Tue May 15 16 06 59 2007 Figure 76 Confirmation of mouse transfer Clickable links for target cage and rack as well as for the target cage card are displayed 68 5 10How to move a cage to another rack Starting from the rack or cage view a whole rack with all mice can be moved to another rack Mice in this cage do not change their cage IDs There is no feature to move all cages of one rack to another rack in one transaction the cages have to be moved one by one Logged in as admin log out Help MausDB DEMO y View mouse 0 mice in cart Home racks amp cages search amp find import reports settings Cage view or view another cage _ Search cage s Cage 0018 placed in rack 1001 01 Projekt_1 contains 2 mice print cage card move cage
36. a cron job to run ntpdate Sao crontab Enter the following line 02 x x usr sbin ntpdate lt time_server gt 2 2 22 Switch off log flushing by the Ubuntu log rotate service By default mysql binary logs are flushed once a day This is done by the log rotate service Binary log files that are generated this way are not copied to a safe place by the backup script Comment out everything in ete logrotate d mysql server to stop this service 16 2 3 Installation of MausDB 2 3 1 Download MausDB installation files Download MausDB_vx x tar gz from http jupiter helmholtz muenchen de Extract downloaded file into home admin mausdb tar xvzf MausDB_vx x tar gz Please make sure that that the resulting directory structure looks like this the following instructions are based on this structure It may be necessary to rename the directory mv mausdb vL 5 mausdb Riemey cman mauscb s6r home admin mausdb SOL check_consistency home admin mausdb SOL delete home admin mausdb SOL insert home admin mausdb SOL setup_database home admin mausdb SOL select home admin mausdb SOL update home admin mausdb code home admin mausdb code var home acma nmy mauedereode wen maus connect home admin mausdb code var www home admin mausdb code var www mausdb home admin mausdb code var www mausdb css home admin mausdb code var www mausdb images home admin mausdb code var www mausdb maustmp home admin mausdb code
37. aestacsacossecedesscadecsseves secagtacseecgouseceucounss ees aE E N 71 Oxted Usine backup SCD iesin sinn 71 5 1 2 ManualDack ps 2 2 71 6 1 3 Restore from DaCKUDaoenosi a A 71 6 2 Blocking user interaction Global lock ssssseecceoccossssssesceeccccococcosssssescccccccccoccosssssssscccccccceececossssssee 71 92 Setting a clobal lock yra web User IM eL FACE a nennen 71 622 Dcn ae obal lock Mmanw ally eirp E EES T2 6 3 Administrational overviews and settings ssssseccocccosssssseccececcccccccossssseeccccccocccccoosssssseececccoceccocessssssee 72 6 4 Administration on database level oooececccccccccccccccccecececeseececeeessceeeeesseeeseseeseseesessessesesesssssssssssssssssso 72 1 Introduction 1 1 Definition purpose and intended use What is MausDB MausDB 1s a laboratory mouse information and management system LMIMS MausDB has been custom developed for the needs and requirements of the German Mouse Clinic GMC It has been published and made freely available for the scientific community Its purpose is to facilitate all aspects of handling laboratory mice e by storing all relevant data of a mouse facility including animal data in one central database e by providing this data to all users simultaneously on a multi user access platform e by ensuring that information is up to date and all users have access to the same information in contrast to working with distributed spreadsheet files
38. age card move cage cage history Current cage color EN Change to blue update color age death genotype strain line lroom rack cage comment shortened move mouse 1 O Booos138 38 f 13 03 2007 ss Ho B 26 1001 01 0018 move mouse 2 O So005139 39 f 13 03 2007 ss y Hn p 8e 1001 01 0018 move mouse Add selected mice to cart What do you want to do with mice selected above mate genotype add change experiment add change cost centre order phenotyping Figure 14 Cage view Basic details of all mice in a cage are displayed along with their clickable mouse ID which will lead to a mouse details view see 4 6 Clicking the move mouse link will start a mouse transfer dialog see 5 9 Again mice can be selected for actions available on the bottom button bar or for being put in the cart see 5 5 Just on top of the mice table there are links for printing a cage card see 4 4 4 for starting a cage transfer dialog see 5 10 or for viewing the history of the cage ID See 4 7 2 The color of the cage card color bar can be adjusted as well 4 4 4 Cage card Cage cards can be printed by clicking on the respective links in the rack view see 4 4 2 and cage view see 4 4 3 1001 01098 0297 1001 01 MMMM 0297 oOOO04 724 74 F 23 01 2007 orig M 402 HIJ B B fa S0003924 y hij F 50004724 24 mo 50003930 50004725 25 23 01 2007 I IN orig M 402 ine fa 5000392
39. aper Being listed in the cart does not affect or change properties of that mouse in the database at all Removing a mouse from the cart also does not affect or remove the mouse from the database The cart content 1 e a set of mice is bound to a browser session which means the user specific cart is emptied after logout However the current cart can be permanently stored to the database Thus grouping of mice is made possible No matter where mice are caged no matter if mice died in the meantime they stay in the cart Logged in as admin log out Help MausDB DEMO Y 2 mice in cart Home racks amp cages search amp find import reports settings empty cart Figure 16 The cart symbol indicates that there are two mice in the cart Clicking on the cart symbol leads to the cart view Logged in as admin flog out Help MausDB DEMO y 2 mice in cart Home racks amp cages search amp find import reports settings empty cart Your mouse shopping cart or There are 2 mice in your shopping cart 3 w Oo a HIJ B B6 1001 01 0012 HIJ m 13 03 2007 55 a y i Hn B B6 1001 01 0012 tt H 1 born age line room rack cage comment shortened Remove selected from cart Keep selected in cart cart name cart_admin_07 05 2007 public O or or Export cart to Excel What do you want to do with mice selected above add change experiment add change cost centre ord
40. ar sex born age death genotype strain line room rack cage comment shortened move mouse 23011998 3399 esveveretnt aac i20 1001701 0296 move mouse Add selected mice to cart Figure 73 Starting a mouse transfer to another cage from the cage view Clicking move mouse on the mostright colum will start the move procedure for that mouse 67 Move mouse Move mouse 50005155 from cage 0296 in rack 1001 01 1 Step please choose target cage move mouse to anew cage or to an existing cage 0005 please enter existing cage id a new cage will be placed this cage will stay where it is in the rack chosen below below rack selection will be ignored 2 Step please choose target rack racks from your screen or all racks 1001 01 Projekt_1 28 free slots 1001 01 Projekt_1 28 free slots optional step please specify move date 15 05 2007 16 05 03 EJ move mouse or cancel go to previous page Figure 74 Target cage definition In the first step the user must decide whether to move the mouse into a new cage or into an existing cage In the new cage scenario the second step defines the target rack for the new cage which is not neccessary when moving into an existing cage The third step defines data and time of the movement Move mouse Please check and confirm if this is the cage where you want your mouse move to Target cage 0005 placed in rack 1001 01 Projekt
41. ate a new mouse project Project info project name Please enter the name of the new mouse strain project shortname Please enter the short name of the new project vo description enter a description for the new project parent project Projekt_1 Please assign a parent project for the new project define new projec Figure 3 Define a project name short name description and parent project may be given 3 4 4 Defining experiments admin function In this context an experiment is a description of examinations that shall be performed on laboratory animals which require a concession from any kind of regulatory authority It is 23 recommended to enter the reference number as experiment name As there are no comment fields the experiment name should be self documenting In order to track experiment assignment of individual mice experiment need to be defined As admin choose settings new experiment Create anew experiment Experiment info experiment name Please enter the name of the new experiment define new experiment am cancel Page generated on Mon Apr 30 14 28 57 2007 Figure 4 Define a new experiment only the experiment name is needed 3 4 5 Defining cost centres admin function You may want to calculate the sum of days mice were housed in your facility in order to charge the costs of animal husbandry to someone In order to track cost centre assignment of individual mi
42. ating 335 show ancestors Breeding record for mouse 50003923 all matings in which mouse 50003923 was is parent Total progeny 70 mating id GE name mating Stat Mag end mung scheme En purpose girati project I itter number komment matina zre ae 2 07 11 2006 ee Projekt 1 1 Genotype information for mouse 50003923 gene genotype genotyping date genotyping method hij Y 09 10 2006 unspecified Properties attributes for mouse 50003923 no properties attributes for this mouse Files available for mouse 500039273 no files stored for this mouse Add mouse to cart What do you want to do with this mouse kill mate genotype add change esperiment add change cost centre order phenotyping Figure 18 Mouse details view On top of the box the edit details link leads to a dialog where some mouse specific details can be modified see Figure 19 Top box the top row contains individual mouse data GVO is the German acronym for genetically modified organism On top of the room rack cage information the cage history link leads to a detailed cage history of the current individual mouse see 4 7 1 Assignment to an experiment and cost centre assignment are given with time ranges Below box the origin information indicates whether a mouse origins from a weaning or from an import For weaned mice links to littermates litter see 4 7 5 parents mating
43. ation construct used background of donor cells background of ES cell line embryo transfer comment External genetic father TNFa 123 cooperation_partner Page generated on Fri May 11 10 48 40 2007 Figure 49 Embryo transfer details view 5 3 How to report litter As soon as newborns are observed they can be reported to the database Litter reporting is a precondition for weaning in MausDB Litter reporting always starts from the mating details page of the mating where litter has to be reported Mating details previous next Parents of mating 492 r entered me left e mfe s E E a aer Bu rn role mating mating mouse ID ear sex born eath genotype strain line room rack cage parental status ES x y FE a z 104 el 6 jE a N a 7 l FR ie wa GE UAR a 1 2007 RL L zj 39 022 de ee 03 HE mus 01 2007 E E Ten AR po E 1002 09 0223 um remove Litters from mating 492 No litters found for mating 492 Details for mating mating 492 Mating type normal mating Mating name Mating start 28 03 2007 Mating end Stop mating 11 05 200713 1329 EJ Stop mating Ans date time for m end Strain Line ABC C3H Mating scheme Mating purpose Mating generation assigned project Projekt_2 mating comment update mating comment Figure 50 Step 1 Report litter for the correct mating Between parents table and mating
44. ation of phenotyping data using the R interface Phenotyping data stored in MausDB can be visualised and statiscally analysed using the custom R interface of MausDB Three steps are necessary and are shown on an example means into same line a a specific SQL script needs to be located in var www mausdb R sudo cp home admin mausdb code var www mausdb R example sql AN var www mausdb R b a specific R script also needs to be located in var www mausdb R sudo cp home admin mausdb code var www mausdb R example r TA var www mausdb R c the two scripts need to be known by MausDB means into same line mysql u lt user gt p lt password gt mausdb lt home admin mausdb SOL insert add_settings_R_scripts sql 44 The entry made here must be the prefix name of the two scripts In th s example example r and example sql require adding example to table settings Please study the example r and example sql for further explanations how the system is working In order to run the script go to the orderlist and press the button apply R script Run R script example on a selection of 9 mice Scatter plot body length body mass vs length Figure 34 Example of phenotype data visualisation using R scripts via the MausDB web interface Please note data has been generated randomly and must not make sense at all 45 4 13 Overviews and reports the reports page 4
45. cal cage Such a detailed rack history of a cage can be easily viewed with MausDB and is available by a link from the respective cage view see 4 4 3 Logged in as admin log out Help MausDB DEMO 1 y view mouse 0 mice in cart Home racks amp cages search amp find import reports settings Rack history of cage ID 0026 Cage ID 0026 was assigned to the following racks in rack from cagemates 1002 152 28 11 2005 12 00 00 alo 08 03 2006 15 34 34 4 50000054 50000054 50000055 1002 12 2 0 08 03 2006 15 35 10 alo 05 04 2006 09 40 115 50000057 1002 13 05 04 2006 10 26 00 03 05 2006 15 08 03 50002626 20002627 50002628 1002 15 03 05 2006 15 08 03 08 05 2006 15 29 22 50002627 100 1 03 29 05 2006 09 39 00 26 06 2006 09 31 16 50002845 1001 03 26 06 2006 09 41 58 13 11 2006 10713 58 50002194 20002884 1002 11 15 11 2006 09 00 00 10 01 2007 10 32 14 50004148 20004149 50004150 50004151 1002 11 10 01 2007 11 10 47 still there 50004022 20004245 Page generated on Thu May 10 13 37 54 2007 Figure 21 Rack history of a cage For a given cage ID the table lists previous and current assignments to racks column 1 with the relevant time range columns 2 3 4 7 3 Ancestor table In order to trace back the ancestors of an individual mouse over generations an ancestor tree is the most convenient way to do so MausDB uses an ancestor table to show parents of mice toge
46. ce cost centres need to be defined As admin choose settings new cost centre Logged in as admin flog out Help MausDB DEMO Yy Wiewmause 0 mice in cart Home racks amp cages search amp find import reports settings Create anew mouse cost centre Cost centre info en cost centre name L Please enter the name of the new cost centre cost centre cost centre number Please enter the number of the new cost centre cs centre description ps enter a description for the new cost centre define new cost centre resetform cancel Page generated on Mon Apr 30 14 30 39 2007 Figure 5 Define a new cost centre name number and description need to be given 3 4 6 Defining users admin function Working as a multi user system with role specific functionality and account specific default views and privileges MausDB requires the definition of user accounts As admin choose settings new user 24 Logged in as admin log out J Help MlausDB DEMO Y C a ptr Home racks amp cages search amp find import reports settings O mice in cart Home search amp find import reports settings Create a new user account MausDE account create new User reset form cancel Page gererated on Mon Apr 30 14 33 15 2007 Figure 6 Define a new user account lots of information can be entered 3 4 7 Defining genotypes admin function In order to assign genotypes to mice the distinc
47. cel column Excel column name remove bodylength bodylength body length of a mouse mm n integer simple 100 Ic vi length remove bodymass bodymass body mass of a mouse g n float simple 25 update parameterset settings Figure 30 Parameterset overview Two parameters are defined columns for Excel upload interface are set up and can be configured via the web user interface 4 10Scheduling phenotyping assays and common tasks In MausDB routine common tasks mate wean ship mice sperm freeze as well as phenotyping assays can be scheduled by scientists or a core team using the so called orderlists An orderlist basically is a list of mice scheduled for a particular task formally called a parameterset with a particular due date A so called workflow is a series of parametersets tasks ordered in a given temporal order This way standard multi step routines like primary phenotyping or cryo preservation workflows can be assigned to groups of mice in one step resulting in a number of orderlists Worklists currently have to be defined on SQL level Example scripts are available in the download repository 42 Orderlist view Orderlist information print orderlist orderlist ID 9616 name wildtype__Sperm freeze__2009 11 23 _rey update orderlist name created by rey created at 23 11 2009 07 09 04 job measure scheduled 23 11 2009 week 48 2009 heduled fo a sg
48. d 10153250 98 new_1000 1001 01 f 17 02 1998 013823 10138242 1 zz ee 9 3 fto be assigned 10153448 01 Inew_1000 1001 0 f 23 01 1998 10142679 1014268 Figure 62 Step 4 Final preview A final preview is displayed Pressing import will start the import transaction Logged in as admin log out Help MausDB DEMO wW View mouse 0 mice in cart Home racks amp cages search amp find import reports settings Import 5 step 5 step import imported mice O BAER a lear sex cotor born age strain line room rack father p mother atier coeant import 50005155 10153249 99 f ha 17 01 1998 3405 c57BL 6 BTNT aBc 129 1001 01 ozssfio sezssfineeae ok o O 50005156 10153250 98 r nd 17 02 1998 3374 c57BL 63 BTNT aBc 129 1001 01 fo296 10138239 10138242 fee 0005157 10153448 o1 f na 23 01 1998 3399 c57BL 63 BTNT aBc 129 1001 01 o296 10142679 10142682 fee Print cage cards and optionally set up matings for mixed cages You may want to print new cage cards for all cages involved in the import Please use the links below You may also want to setup matings for all cages containing both males and females Optional set up mating s in separate windows first then print cage card s mating setup dialog will open in new window print card for cage 0296 Import successful You may wantto see imported mice here Add selected
49. details box the button report new litter can be used to report litter for the current mating 55 Logged in as admin log out Help MausDB DEMO y View mouse 2 mice in cart Home racks amp cages search amp find import reports settings empty cart Report new litter for mating 492 1 Step Please specify parents for this litter Using all parents of this mating as default please uncheck mothers that can be excluded E T entered left mo i E ac 2 parent role mating mating mouse ID lear sex born eath genotype strain line room rack cage j28 03 2007 5000477 76 76 m 29 01 102 A e Ss e a 2 Step Please enter litter details date of birth 11 05 2007 132300 Gd please enter date of birth dd mm yyyy hhimm ss total female living pups 0 5 a male female dead 0 Br 7 any anen why reduced litter comment Report litter Pagi generated on Fri May 11 13 21 10 2007 Figure 51 Step 2 Specifying litter details In the upper table parents have to be assigned to the litter If for example a double mating one male two females has been setup and there is clear evidence for one female being the mother of newborns the other female mouse can be unchecked to state it is not the mother In the second box date of birth has to be entered Numbers for observed newborns as well as a litter comment can be entered below Litter report is finished by pres
50. e a fully functional MausDB server can be installed on any machine from scratch within 60 90 minutes This includes a complete installation of Ubuntu Linux installation and setup of MausDB and restoring an initial database Conventions In the following instructions two conventions apply indicates that a command needs to be continued on the same line lt gt indicates a variable for example a user defined password 2 2 Setting up a Linux system as MausDB server 2 2 1 Standard installation of Ubuntu Linux 8 04 LTS server edition from CD The server version of Ubuntu is recommended Installation CD ISO mages can be downloaded from http www ubuntu com Other Ubuntu versions will most probably work as well but may require slight modifications as package names may be different It is recommended to set up a user admin This user must belong to the group admin which is neccessary to obtain root privileges using sudo When using the sudo command you will be asked for a password Please provide the password of admin here When asked for the local time you may enter automatic and enter a time server address When using a multiple hard disk system we recommend the following setup dev sdal dev sdb 1 mysql database separated from operating system After finishing the Ubuntu standard installation networking must work unless the following steps cannot be accomplished This installation guide assumes that the f
51. e the size of the cage pool corresponds to the total capacity of all racks defined As admin choose settings new cages Define new cages Please specify RES Searle 100 you vant to define 100 Pease enter the number of cages to be defined in the database new cages 5 R i y ae at e cages hata a CABEAN Tor pos specify the cage capacity max number of mice per cage 5 mice cages O yes Q no _ Please specify if the cages should be active or not Not active means that the cage are active example yes if the cages should be active defined but cannot be used in MausDB immediately E define new cages resetform cancel Figure 2 Defining new cages Please take care that the total number of cages corresponds to the total rack capacity 3 4 3 Defining projects admin function MausDB uses projects in two ways Every user is assigned to one ore more projects Every rack and every mating is assigned to exactly one project In this context project affiliation determines the view on racks and matings a user gets after logging in Per default a filter is set so that only those racks are shown that belong to user s projects At any time every user can decide to view all other racks too The same is true for matings Phenotype results are strictly managed by projects They are only presented to the user 1f they belong to a user s project or 1f they are public As admin choose settings new project Cre
52. e by providing useful overviews and search functions Its intended use is to comprehensively manage mouse houses ranging from one rack only up to large mouse facilites hosting tens of thousands of mice 1 2 Technical information MausDB is a web based CGI application built on Linux Apache MySQL and Perl LAMP As MausDB works with database transactions t makes use of the InnoDB storage engine provided by MySQL MausDB should also work with any other transactional storage engine or transactional database management system e g PostgreSQL in principle Though this has not been tested at all it might be neccessary to adapt SQL statements in order to fully comply with SQL standards or RDBMS specific SQL dialects In order to avoid dependency from a single database management system the whole business logic has been implemented on application level rather than on database level i e stored procedures Helmholtz Zentrum Miinchen German Resarch Center for Environmental Health GmbH Institute of Experimental Genetics Ingolst dter Landstr 1 D 85764 Neuherberg Germany i Maier H Lengger C Simic B Fuchs H Gailus Durner V Hrab de Angelis M MausDB an open source application for phenotype data and mouse colony management in large scale mouse phenotyping projects BMC Bioinformatics 2008 9 169 6 1 3 MausDB features MausDB covers most aspects of handling laboratory mice for scientific purposes including
53. e put in the cart where the mate button is also available 50 5 1 2 Step 2 Defining mating details In the second step of the mating procedure mating details need to be defined by the user In addition mating partners are checked automatically if they are qualified for mating are they still alive One male at least one female Minimum age of xx days Logged in as admin log out Help MausDB DEMO Aw View mouse 0 mice in cart Home racks amp cages search amp find import reports settings New mating Checking mating partners e checking male mouse 50005140 for mating ok e checking female mouse 50005146 for mating ok Now specify some mating details Grey fields are mandatory please check them carefully White fields are optional and may be left empty please choose rack for mating cage racks from your screen or all racks or J Esant mure 1001 04 Projekt_ 1 38 free slots 1001 04 Projekt_ 1 38 free slots el strain strain that litter from this mating will be new strain optional for new strain only name of 129xC57BL 6 assigned to ain line line that litter from this mating will be HIJ B B6 optional for new line only name of the new line assigned to matter 10 05 2007 16 40 33 ate of mating mating project your screens projects only or all screens projects assign a screen project Projekt_1 O Projekt_l optional mating name give your
54. eeeeeeeeas 17 2 3 2 Settings based on a typical Ubuntu installation cccsssesseseeeeecceeeeeeceeeeeaaeseeseeeeeeeeeeeeeeeeeaaas 17 23 93 Install the Maus DB script TE Srii alba Ga di 18 23 4 Config ration of MausDB scis E E E ee 18 2 3 5 Create the directories for the backup system eccssesssssssseeeeeeenennnnnnnnnnnnnnnnnnnnnnnnnnnnnnnsnnsnnnsnnnnnnnnnnnnn 18 230 Installation of the BACKUP ESCH PE ana ar n e ENEE rE 18 2 3 7 Installation of the checkup script for daily control of database integrity ccccseseeeeeeeeeeeeeeeees 19 3 SETTING UP A NEW MOUSE FACILITY FOR ADMIN USERS 20 3 1 Restoring from a backup dump file cccccccccsssssssvesssssoovccccccoscvsssscsessssseessssssovosacccnsecsssssssseeessssoosss 20 3 2 Starine rom scr tich A Eee 20 32 1 reale the Why SOL Qatabase seinen een 20 3 2 2 Creating database tables and functions using DDL scripts ueeeeeessssssssnnnnnnnnnnssseneeeeneennnnnnnnnnnnn 20 32 3 koadan tlalsetinss mio database aan eek 21 3 3 Loceme in to MausDB as admin esiecacevsccescesccesedessbensesessecescvccceostessaseasecassvsecesuvecseoceeseusadeesbeessteseecees 22 3 4 DGMNING VOU MOUSE ad hy neen neee AAE EEEN OASES 22 3 4 1 Defining rooms and racks admin function ccccceccecceccccceeeceeeeaaeeessssseseeeceeeeseeeeeeaaaasssnseeeeseeeeess 22 3 42 Deine Cases din Michon 2er 23 S45 Deimms projects admin UNCON seele 23 344 Def
55. ent female mouse must have a mouse ID 1 e be defined in MausDB Your mouse shopping cart Oo There are 2 mice in your shopping cart e C mouse 1D lear sex born age death genotype ype strain line room rack room rack cage comment shortened i Eomssaofso F Ianszone aaa y T en 1001 01 0005 Bl amsume gt elm soseo ar ae a Empty cart Remove selected from cart Keep selected in cart cart name cart_admin_11 05 2007 public C or or Export cart to Excel What do you want to do with mice selected above mate embryotransfer add change experiment add change cost centre order phenotyping view phenotyping data upload and link file to selected mice i v select random subset Page generated on Fri May 11 10 22 52 2007 Figure 45 Step 1 Select a female embryo recipient mouse in the cart Optionally also select the biological father mouse sperm donor if available in MausDB Start embryo transfer procedure by clicking the embro ytransfer button in the bottom task bar 32 Logged in as admin lag out Help hausDB DEMO Ww View mouse enge Home racks amp cages search amp find import reports settings empty cart New embryo transfer Checking selected mice checking recipient mother 50003930 for use in embryo transfer a ak Now specify some embryo transfer details Grey fields are mandatory please check them carefully White fields are optional and
56. er phenotyping view phenotyping data upload and link file to selected mice 8 Page generated on Mon May 7 17 44 26 2007 Figure 17 The cart All mice in the cart are displayed one per row Mouse ID room rack and cage numbers are clickable and lead to the respective detail views Cart management functions are available directly below the mouse table Mouse specific functions are made available on the lower part They are either self explaining or explained in detail elsewhere in this manual 33 4 6 Allabout a mouse the Mouse details page Since the mouse ID is the unique identifier of a mouse in MausDB it is displayed as a clickable link almost everywhere Clicking on the mouse ID will directly lead to the mouse details view Mouse details Details for mouse 50003923 edit details mouse ID lear sex born age Jteath genotype strain line generation color is GYO ERE 50003923 23 m fa 08 2008 237 y Huep pa s ma y 100101 009596 Experiment history m From To 234 47 234 47 08 05 2007 10 56 08 still in amp xperiment gt cost centre nen status help MausbB_account_1 09 10 2006 09 00 00 still nen fencer rina no Io phenotyping orders for this mouse Io phenotyping orders for this mouse for this mouse E peaa phepnotyprag no phenotyping records for this mouse no comments for this mouse comments update comment Origin of mouse 50003923 1 litter from m
57. eriment 234 A7 at 15 05 2007 15 47 17 mouse id lear sex 50005155 add change experiment Figure 71 Step 2 Final preview Pressing add change experiment will finalize the procedure Add mice to experiment or change experiment 3 step Trying to add experiment information mouse id lear sex experiment remark 50005155 ss If 234 A7 added mouse to experiment 50005156 ss f 234 47 added mouse to experiment 50005157 oil f 234 A7 added mouse to experiment All done please check remarks for error messages Page generated on Tue May 15 15 48 42 2007 Figure 72 Step 3 Confirmation The remarks column may contain error messages 5 9 How to move a mouse to another cage Starting from the rack or cage view mice can be transferred to other cages There a two cases a moving a mouse to an empty cage A new cage ID must be assigned and a rack must be assigned to this cage b moving a mouse to a cage with other mice that is already in use Cage ID and rack assignment are already defined Logged in as admin log out Help MausDB DEMO zan Y view mouse 3 mice in cart Home racks amp cages search amp find import reports settings empty cart Cage view or view another cage i Search cagefs Cage 0296 placed in rack 1001 01 Projekt_1 contains 3 mice rintcage card movecage rack history of cage ID Current cage color Change to yellow update color ouse ID e
58. ettings block and suitable if entry setup cron job to run backup pl automatically sudo crontab e Enter the following lines means into same line 0 23 usr bin perl home admin backup backup pl do_backup yes gt gt home admin backup backup log 0 8 18 1 5 usr bin perl home admin backup backup pl flush_bin_logs yes gt gt home admin backup backup log will run a full dump at 23 00 every night will flush binary logs every hour at 8 00 18 00 at monday friday 2 3 7 Installation of the checkup script for daily control of database integrity copy checkup script and set appropriate ownerships cd home admin backup cp home admin mausdb services checkup pl CA sudo chown R admin admin backup SF SF OSE adapt settings in backup pl according to your system and paths see above sudo nano backup checkup pl In order to setup cron job to run checkup pl automatically proceed as described above for backup script At this point all software needed to run MausDB should be installed and configured on your system The following steps describe how to set up a MausDB installation 19 3 Setting up a new mouse facility for admin users 3 1 Restoring from a backup dump file In case you had MausDB already running and need to restore the database from a dump file on a different server mysql u lt username gt p lt password gt mausdb lt dumpfile sgl If all your data is contained in dum
59. flow management and worklist scheduling mysql u lt user gt p lt password gt mausdb lt home admin mausdb SOL setup_database parametersets sql 21 3 3 Logging in to MausDB as admin Assuming you installed MausDB on a computer named mausdbwww following the instructions given in this manual you should be able to log in to the inital system Just use Mozilla Firefox to access the following URL http mausdbwww yourdomain cgi bin mausdb mausdb cgi Enter admin as username and mausdb as password these have been defined in the previous step see above Don t forget to change the password as soon as possible 3 4 Defining your mouse facility In this step all settings that are specific to your mouse facility need to be defined 3 4 1 Defining rooms and racks admin function As MausDB manages all rooms racks and cages of your mouse facility the racks must be defined beforehand As admin choose settings new rack Logged in as admin flog out Help MausDB DEMO y Wiewmouse 0 mice in cart Home racks amp cages search amp find import reports settings Define a new rack Please specify details for your new rack rack name eee a Please enter the name of the new rack jexample 01 for rack 01 in room 1234 ea Please specify the room in which the rack is placed example 1234 if rack is placed in room in room 1234 building be Please specify the building in which the rack
60. g of mice can be started for one mouse from the mouse details page or for multiple mice from the cart cage or rack view Logged in as admin log out Help MausDB DEMO e Y View mouse 0 mice in cart Home racks amp cages search amp find import reports settings Cage view or view another cage Search cage s Cage 0018 placed in rack 1001 04 Projekt_1 contains 2 mice rint cage card move cage rack history of cage ID Current cage color EEE Change to blue v update color O mouse ID lear sex born age death genotype strain line lroom rack cage comment shortened move mouse 1 Booos138 38 f 13 03 2007 63 v Ho B6 1001 04 0018 move mouse 2 Sooos139 39 f 13 03 2007 63 v Ho B B6 1001 04 0018 move mouse Add selected mice to cart What do you want to do with mice selected above add change experiment add change cost centre order phenotyping Figure 80 Starting from the cage view mice subject to culling are selected using the checkboxes Pressing kill in the bottom functions bar will lead to the next step Kill Please confirm killing of animal s listed below e selected for killing mouse 50005138 e selected for killing mouse 50005139 and choose killing reasons Date and time of death 15 05 2007 16 51 13 Killing reason how killed v v Figure 81 Defining culling date and culling reasons Pressing confirm kill wi
61. ge and genotype by genotype from line ABC 129 M5 1 genotype a abc SEH male or female 2 genotype Fi ae a e from no min age kai to roras Mi g a a 3 genotype a abc t i Hi genotype any Search by genotype include dead only dead Search by line and sex by mouse comment a by experiment by patho IDfs a by foreign ID 2447 v Search by comment Search by experiment b Search by foreign iD Search by patho ID by strain strain include dead Search by strain Find mating by ID a Mating s by name a Mating s by project matings by Frojekt_ 1 e ABC 123 Search by mating ID Search by mating name Search Search by mating project er project Search Search by mating line Hatin en litter by ID Import by ID te orderlist by ID orderlists PTE Kil done Search by litter ID Search Search by import ID import ID E Search by orderlist ID orderlist ID Searched orderlists Search orderlists by parameterset natamelerseh cart by cart name file s by keyword Search files by keyword Figure 26 Search amp Find page Top section Clicking browse matings leads to a mating overview see 4 8 1 clicking browse imports leads to an import overview see 4 8 2 Middle section Mice can be searched for by different criteria The result set will always be a list of mice Optionally searches in th
62. gned at weaning or import time may change In the mouse details page see 4 6 or the cart the bottom function bar contains a button add change cost centre see below What do you want to do with this mouse add change experiment add change cost centre order phenotyping Page generated on Tue May 15 15 28 42 2007 Figure 68 The standard function bar that is available on the bottom of the mouse details page the rack and cage view and the cart 65 Logged in as admin log out Help MausDB DEMO Y View mouse 3 mice in cart Home racks amp cages search amp find import reports settings empty cart Add mice to cost centre or change cost centre 1 step Please choose the cost entre you wish chosen mice to be added or changed to see cost centres overview Cost centre MausDB_account_l Date on aN T at which mice entered new cost centre 15 05 2007 15 30 01 a mouse id ear sex cost centre 50005 155 3q f mouse already already is assigned to a cost centre If you continue the cost centre will be updated confirm cost centre Figure 69 Changing the cost centre for a mouse The new cost centre can be selected from a pulldown menu The date of cost centre change must be given The current cost centre assignment is displayed Pressing the confirm cost centre button will lead to a preview page where the procedure can be finalized 5 8 How to change experiment status of m
63. ice the cart cce 00000000sssssanuennnunununnssssssssssssssssssssnsnsnnnnssssssssssssssssssssseee 33 4 6 All about a mouse the Mouse details page cccccssssssssssssssscscscccccccccccccccssssssscssscscccccscsssssesess 34 4 7 Some More informalional views ee 35 Adel Case History Or MOUS Herren 35 2 72 Rack history Ola CACC naeh rauhen 36 AiO Aee SOLAD E een 36 2 74 Manno detale VIEW ciran a Men 37 3 VER Wile WW Seen een een 38 47 0 INDORE vie Werner edel 39 4 8 Finding mice by properties the search amp find page ssssscscsccccccccssssssssssssssssccsccscccccccsssssseees 40 dab Mine OVNE N eeen a een 41 BSc TMPO CVE nee nee sed ond burt austinnumnatatle N adnadteak ie aees 41 4 9 Managing your phenotyping data Parametersets scssssssscssssccccccccccsssssssssssccsccscccccccssssessees 42 4 10 Scheduling phenotyping assays and common tasks ccccccccccssssssssssssssscsssccccccccccccsecssssssssscsscssscsooes 42 4 11 Loading phenotype data into MausDB ssssssscssscccccccccccccsssssssssssccccccccccccccccssccsssssssssssssssssscees 43 4 12 Statistics and visualisation of phenotyping data using the R interface 00000000000000000000000000000 44 4 13 Overviews and reports the reports Page 000sss000000000000000000s00000ssssssssssssnnsnsnnnnnsssssssssssssssssssssee 46 4 13 1 Mouse lines OV CLV Wasser nenne een 46 4 13 2 M
64. ice According to German law mice that are subject to experiments must be reported The normal case in MausDB is defined as breeding When a mouse starts into an experiment date of experiment start and the experiment itself must be reported At any time a mouse can be assigned to no or one experiment However during lifetime of a mouse it can be assigned to several consecutive experiments As with cost centre assignment see 5 7 this can be done for one mouse from the mouse details page or for multiple mice from the cart cage or rack view Logged in as admin log out Help MausDB DEMO W View mouse 3 mice in cart Home racks amp cages search amp find import reports settings empty cart Add mice to experiment or change experiment 1 step Please choose the experiment you wish chosen mice to be added or changed to Experiment 234 47 v Date A7 3 at which mice entered new experiment 15 05 2007 15 47 17 d z mouse id lear sex experiment status 50005155 99 f breeding animal 50005156 s8 f breeding animal 50005157 01 f breeding animal confirm experiment Figure 70 Step 1 Defining experiment and start date The current status of selected mice is shown in the bottom box Pressing confirm experiment leads to a preview page where the procedure can be finalized 66 Add mice to experiment or change experiment 2 step Please confirm adding the mice listed below to exp
65. in MausDB It is the main and unique identifier of a mouse in the system Every mouse specific data and information is attached to the mouse ID In other words there is no concept of anonymous mice in MausDB The same is true for all other entities in MausDB where entity means a data representation of physical rooms racks cages or abstract matings projects objects 4 1 2 How mice get into MausDB import and weaning A mouse can enter MausDB in either of three ways e by import from an external source All mouse specific properties have to be defined at import time e by weaning litter where litter is defined as the set of siblings originating from a mating that has been defined in MausDB Most properties are inherited e by embryo transfer which is a special case of mating weaning 4 1 3 Two worlds real world vs database world As every other comparable database application MausDB uses a structured database model of the real world i e the physical mice cages racks rooms and other relevant things like users projects genotypes to store link and display data Of course a precondition for proper function of MausDB is congruence of information in both worlds For example a mouse is physically moved from cage 1234 to cage 2345 After that real world action this cage transfer has also to be performed in the database world i e MausDB in order to reconstitute a proper database
66. ining experiments admin Tuncton kasieea ae a EA 23 54 5 Deiinins cost centes admin TUNCHON euere 24 3 46 Dehnims users admin WNOHON Neem 24 3 4 7 Detinine genotypes admin Tuncion eusaneei I ee eee 25 3 4 8 Configuring email address es for admin user s ceccccccceccceeceeesseeesseeeeeeeceeeeceeeceeeeeeaaasaessseeseeeeeeess 26 4 WORKING WITH MAUSDB FOR ALL USERS 2 220 200 2000n0nnnonnnnnnnn 27 4 1 Some Dasic COMCE PIS a une ascitic denen chee aE recited chan eds SA EaR acca uncecenened ecutenes 27 4 Evenn hasan ID esse een eisen tete 21 4 1 2 How mice get into MausDB import and weaning ueeeessssssssnnnnnnnnnnnsssnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnen 21 4 1 3 Two worlds real world vs database World iiss u a a a 21 4 2 Getting Started a ee ee ee essen nlsadats 28 42 1 21208910 into Mais DB zer ee LE Ans enihelte 28 4227 gt lien TO Sai W ee RT RR LT EP POE WRLC ZO CO UU a a 28 42 5 SChanshe Te PASS WOE eek nee eh 29 4 3 The Quickfinder tool find mice and Cages 0 000000000000000000000000000sssssnnununnnnnnssssssssssssssssssssnsnnnnnnse 30 4 4 Locating mice browse racks amp cages esssssssssennssssssenssnsnnnssssnnnsnnnsnssnnsssssssnnsnnnnnnsssnnnssssnnssssssssnnnnnnnee 30 44 1 Rack OV CE VIC We arte ea eat 30 442 Rack WAC WY seas ees excise case een 30 44 3 SC AOC NIC Wear ee eal E 31 444 BIS cal ek leakiken 32 4 5 Collecting and Grouping m
67. is section can be restricted to mice currently in the cart which allows concatenation of different searches The input fields by mouse ID s and by cage ID s accept any input for example a whole spreadsheet colum copied via the clipboard IDs contained in this input will be recognized automatically Bottom section Other entities than mice can be searched in this section for example matings imports carts and others Searches in this section cannot be restricted to the cart Input fields for name or comment searches accept multiple terms that are combined by logical AND 40 4 8 1 Mating overview All matings ever set up in MausDB can be listed in the mating overview Mating overview 7 quick find Search by mating ID Found 492 matings Select all matings or only active matings Browse pages first previous next last mating id ET name mating foe DT end strain line momi scheme matagi purpose REIT project fi itter number comment 1 mating 492 492 2 28 03 2007 ABC C3H Projekt_ 2 0 2 mating 491 491 28 03 2007 ABC C3H Projekt_ 2 0 3 mating 490 490 o 26 03 2007 26 03 2007 ABC FLP CON Projekt_ 2 0 4 mating 489 459 26 03 2007 ABC FLP con Projekt_ 2 0 matin 48 26 03 2007 ABC FLP CON Projekt_ 2 0 matin 48 26 03 2007 SER BTNT KLM KO Projekt_ 2 0 mating 48 26 03 2007
68. is placed example 35 if rack is placed in a room in building 35 subbuilding SUSIE else rennin subbulding amp Peas specify the subbuilding in which the rack is placed of building 35 Capacity Please specify the rack capacity max number of cages in this rack example 42 if the rack has a capacity for 42 cages Pe park achive Oves Ona Please specify ifthe rack is active or not Not active means that the rack project Frojekt_1 Please choose the project to which the rack is assigned Oves Ono Please specify if the rack is internal or not Internal means that mice in BAUER EENIA Ores yes this rack live outside your facility end Sa ee Optional Please enter a code for the facility in which the new rack is rack Code example 1300 if the code for this animal facility is placed 1200 rack comment or description example mating rack define new rack resetform Optional Please enter a comment for the new rack Figure 1 Defining a new rack by entering rack specific information Please take care that the total number of cages corresponds to the total rack capacity 22 3 4 2 Defining cages admin function As MausDB manages all rooms racks and cages of your mouse fac l ty the cages the cage pool must be defined beforehand MausDB does not manage individual physical cages but a pool of cages that are tagged with a cage id Therefore it is required that the number of cages defined 1
69. jekti 3 40 23 17 era 52 Projekti 40 00 40 0 Projekt_1 40 24 16 HERE KERRERRERREREEREEE 46 Projekti a BE 40 Dii 6 66 Projekt_1 26 Projekt_1 cages 162 198 total mice 353 Page generated on Mon May 7 14 29 25 2007 wale ae a I jm jw Oo 71710 iO 77 A 1 79 CO jo jo CO ia Figure 12 The rack overview lists all user assigned racks per default The leftmost column contains clickable rack links ordered by room The second column shows the rack capacity number of cage slots 4 4 22 Rack view Following a link from the rack overview an individual rack with all current cages can be displayed 30 Rack details 2 Overview rack 01 in room 35 Floor_A 1001 4 Cages _ total number total F of mice in project Sn mia capacity in use free ee in use and free cages this rack nee y u a nyes Terre we rererere 28 Projekt_1 Cages currently in this rack expand all cage info cage action click for details Jear sex ve born age genotype strain line move print ETA 0005 1 female strain line HIJ B B6 cage e print card int card gt mal rain line HII B B6 lesa Th Hine card 0018 0018 2 females strain line HIJ B B6 1 jol 50005138 es fi 03 2007 2 O 50005139 as I 03 2007 0096 1 male 1 female strain line HIJ B B6 4 females strain line HIJ B B6 e
70. l file Data can be controlled and edited if neccessary Logged in as admin log out Help MausDB DEMO Y Vewmouss 0 mice in cart Home racks amp cages search find import reports settings Import 3 step 3 step check update form data MausDB ID external ID ear tag cage rack sex born father 1 mother 2 mother comment remark 1 to be 10153249 99 Inew_1000 S2 ct rack f 17 01 1998 10138235 10138242 E g Zi assigned A IL below L AIL i i IL IL SEE 10153250 se _ new_1oo0 Belek Tr 17 02 1998 10136235 10136242 if assigned alone 10153448 o1 Inew_ ooo jseletrack 23 01 1998 1014267s 10142682 _ IE ee Doido anois bankas update import preview choose racks for new cages cage rack info all cages 1001 01 Projekt_1 29 free slots choose rack for all cages Inew_1000 E 001 01 Projekt_1 29 free slots i E female s update import preview Figure 61 Step 3 Eartag and cage assignment See Figure 55 for explanation 62 Logged in as admin log out Help MausDB DEMO Y View mouse 0 mice in cart Home racks amp cages search amp find import reports settings Import 4 step 4 step confirm import data MausDB ID external ID jear tag cage rack sex born father 1 mother 2 mother comment remar alto be assigned 10153249 99 new_1000 1001 01 f 17 01 1998 10138239 10138242 2 to be assigne
71. l perl sudo env FTP_PASSIVE 1 cpan cpan gt install GD Barcode Spreadsheet WriteExcel Simple sudo env FTP_PASSIVE 1 cpan cpan gt install Spreadsheet WriteExcel Simple spreadsheet ParseExcel sudo env FTP_PASSIVE 1 cpan cpan gt install Spreadsheet ParseExcel Simple Array Iransp se sudo env FTP_PASSIVE 1 cpan cpan gt install Array Transpose remark Test Pod Coverage this may require installation of modules Test Pod and 2 2 19 Installation of packages required for statistics and visualisation 15 Install R sudo apt get install r base Install additional CRAN modules via apt sudo sudo sudo sudo sudo sudo sudo sudo FF HHH H H ape ger apt get ap Ger apt get apt get apt get apt get ape get inetal install install install install install install Install r cran tseries r cran lattice r Chana dba r eran rnysgLl r eran gdata r cran gmodels recla g LOCS r cran gregmisc 2 2 20 Install xvfb Virtual Framebuffer fake X server sudo apt get install xvfb may be required add path to xvfb to xvfb run sudo nano usr bin xvfb run Look for line PATH add bin to the path It should read PATH SPATH usr biny X 1 usr xX 1 1 R6 bin bin 2 2 21 Synchronize the system time to a time server remark the following step can be skipped if synchronization to a time server has been choosen during installation of Ubuntu Set up
72. ll finalize the procedure Kill Killing animal s listed below How killed Why breeeding excess e trying to kill mouse 50005138 successfull e trying to kill mouse 50005139 successfull Page generated on Tue May 15 16 52 03 2007 Figure 82 Confirmation of culling 70 6 MausDB Administration 6 1 Backup database 6 1 1 Using backup script Fully automated backups can be scheduled by using the backup scr pt described n 2 3 6 6 1 2 Manual backups At any time a full dump of the database can be done manually mysqldump opt u lt username gt p lt password gt mausdb gt dumpfile sql Please note th s may take some minutes 6 1 3 Restore from backup A database can be restored from a full dump WARNING this will overwrite your current database mysql u lt username gt p lt password gt mausdb lt dumpfile sql Please note th s may take considerable time depending on the s ze of your database For more sophisticated restore scenarios like point in time recovery please check the MySQL documentation 6 2 Blocking user interaction Global lock There is a mechanism called global lock implemented in MausDB that stops user interaction via the web user interface It is strongly advised to set a global lock in two situations o when damage to the database occured e g by manipulation on database level Immediately after a database damage occured or s noticed a global
73. mating a unique name optional mating scheme inbred outcross optional mating purpose your own description optional generation something like F1 F2 optional comment any comment cancel mating go to previous page Page generated on Thu May 10 16 40 33 2007 Figure 43 Step 2 Defining mating details Per default a mating is automatically set up in a new cage where mice are put together As a consequence the user can choose the rack in the first table row Alternatively checking the don t move box will cause MausDB to leave mating partners where they are Strain genetic background of mating offspring needs to be chosen in the second table row from a pulldown menu Alternatively a new strain can be defined by choosing new strain in the pulldown menu and entering a new strain in the input field The same procedures applies for mouse line selection in the third table row Mating date refers to the date when the mating really started Defining a mating project will remember project assigned users about litter weaning Other fields can be optionally filled by users Pressing the mate button will finally set up the mating and present a confirmation page see below 5 1 3 Step 3 Confirmation If the mating could be successfully set up in the database a confirmation page is displayed 51 Logged in as admin log out Help MausDB DEMO y Wewmouse 0 mice in cart Home racks amp cages
74. may be left empty date of embryo transfer 11 05 2007 10 3422 BJ a NEE CS57BLEJ w optional for new strain only name of the new strain on new line w optional tor new line only name of the new line TNFeKO embryo ID TNFa t 2307 origin a i Cee 2 in wind method fe 3 5 embryo production En Fy u She Erw eos iced Fa P sperm fresh I frozen assisted IVF none Laserivr Orcs embryo preservation oy e fresh revitalized no manipulation in house gt knockout blastocyst injection background of donor cells background of ES cell line transgenic manipulation mi has She embryo boon m i name of construct line 0 transgenic animal pronucleus injection background of donor cells name of construct line recipient mother s 50003330 genetic father internal genetic father extemal erternal mouse ID EI NFa 123 origin cooperation_partner anbe banionpro erk your screens projects only or allscreens projects Projekt_1 C Projekt_1 v optional embryo transfer name ee VE optional embryo transfer purpose el GG optional comment setup transfer cancel embryo transfer go to previous page Figure 46 Step 2 Defining embryo transfer details Embryo transfer date refers to the date when the embryo really was implanted Strain genetic background of mating offspring needs to be chosen in the
75. mice to cart Page generated on Tue May 15 14 39 35 2007 Figure 63 Step 5 Confirmation As the import has been completed mouse and cage IDs are available and are displayed as clickable links Links to cage cards are displayed for every cage If import leads to mixed males and females cages matings can be set up quickly by following optional links 5 6 How to genotype mice In MausDB genotyping a mouse means to ass gn a locus related genotype term to a mouse As multiple genotypes can be managed by MausDB a combination of locus marker e g TNFalpha and genotype term e g is stored In the following example three mice from the previous import example have been put in the cart 63 Logged in as admin log out Help MausDB DEMO _ y O ee 3 mice in cart Home racks amp cages search amp find import reports settings empty cart Your mouse shopping cart or There are 3 mice in your shopping cart a at 01 1998 3405 02 1998 3374 a strain room rack cage comment shortened ENE ABC 129 1001 01 0296 Esrewssamr asc 2s 1001010256 01 1998 3399 CS7BL 6 BTNT ABC 129 1001 01 029 beim ear sex born a je strain line room rack cage comment shortened Remove selected from cart Keep selected in cart cart name cart_admin_1 5 05 2007 public L or or Export cartto Excel not as U oO ne Jaan HE TE m i M w
76. mouse housing costs to MausDB_account_1 v how many pups from this litter do you want to wean EEEa O1 O2 O3 O4 O5 101 O2 O3 04 O5 01 v in one cage only applies for new cages only applies for new cages optional wil start ear tag 0 WE optional use existing cages example 13 543 8 876 example 17 0548 89 optional litter comment or go back Figure 54 Step 2 Defining litter details In the third and fourth row date of birth and weaning need to be controlled In most cases weaning type should be regular Mice can be weaned as external mice if they need to be managed by MausDB e g for data completeness or family relationship preservation but do live in rooms racks that are outside the facility which is managed by MausDB Important external mice are not taken into account when calculating mouse days see 4 13 6 or numbers for the TEP report see 4 13 3 The numbers of males and females are automatically set from previous litter reporting but can be changed in this dialog The maximum number of mice per cage can be selected If males should be caged individually the number would be set to 1 In the course of weaning eartags are incrementally assigned starting from the given number Alternatively it can be set to consist of the last two digits of the mouse ID by choosing by ID in the pulldown menu In order to fill up existing cages cages currently in use the correspondent cage
77. mouse information and management system Copyright C 2008 Helmholtz Zentrum M nchen German Research Center for Environmental Health This program is free software you can redistribute it and or modify it under the terms of the GNU General Public License as published by the Free Software Foundation either version 2 of the License or at your option any later version This program is distributed in the hope that it will be useful but WITHOUT ANY WARRANTY without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE See the GNU General Public License for more details You should have received a copy of the GNU General Public License along with this program if not write to the Free Software Foundation Inc 51 Franklin St Fifth Floor Boston MA 02110 USA 1 5 Before using MausDB Carefully read the GNU General Public Licence see above under which MausDB has been made available before using MausDB Please pay particular attention to what the license says about warranty liability and risk of use 2 Installation 2 1 Before you start This installation guide is based on the use of Ubuntu Linux version 8 04 LTS server edition It is possible to install MausDB on other systems as well succesfully tested with Mac OS X Package installation procedures pathes and settings may vary and must be adapted when installing MausDB on other systems Time required Following this installation guid
78. nd females are moved into the same cage On the other hand once a mating is defined it will not be stopped automatically upon separation of the animals 5 1 1 Step 1 Defining mating partners In order to define the mating partners one male one or more females these must be selected first either in the rack view see 4 4 2 or after having collected them in the cart see 4 5 Logged in as admin log out Help MausDB DEMO l y 0 mice in cart Home racks amp cages search amp find import reports settings Rack details 2 Overview rack 04 in room 35 Floor_A 1001 Cages total number total k of mice in project assignment info capacity in use free cages in use and free cages this rack 40 2738 ere tte A ae a Cages currently in this rack collapse all cage info cage action u born Ir Ls genotype mo strain a line print Par eal sooosiae ser feroa 2 O 50005147 7 15 03 2007 5 gt OL msa se iss Add selected mice to cart What do you want to do with mice selected above genotype add change experiment add change cost centre order phenotyping Page generated on Thu May 10 16 17 45 2007 Figure 42 Step 1 Defining mating partners In the expanded rack view see 4 4 2 mating partners are selected by checking the box in the first column The mate button on the page bottom directly leads to step 2 Alternatively selected mice can b
79. o cpan or sudo perl MCPAN e shell Initial configuration When starting CPAN for the first time you need to answer some questions which are self explanatory If cpan is slow try using passive ftp sudo env FTP_PASSIVE 1 cpan Net FTP Attention When asked for Policy on building prerequisites follow ask or ignore ask answer follow Installing Perl modules using CPAN porn aliases Denes Celle 2 2 18 Installation of additional packages and Perl modules If installation via CPAN fails pre compiled modules can be installed from the Ubuntu package repository Example sudo apt get install libdate calc perl The following packages are neccessary in order to run MausDB via apt perl GD pre compiled Perl GD Modul sudo apt get install libgd gd2 perl libgd devel sudo apt get install libgd2 xpm dev 14 smbfs sudo apt get install DBI with DBD mysgl sudo CGT pm sudo sudo apt get apE Get apt get CGI Session sudo apt get Date Calc sudo apt get gt MD5 Digest sudo Mail Sendmail sudo ape ger apt get DBD Excel sudo apE gel via CPAN GD Barcode install install install install install install install install smbfs libdbd mysql perl i begr perl libcgi pm perl if above fails libcgi session perl libdate calc perl libmd5 perl libmail sendmail perl libdbd exce
80. o which the genotype refers must be chosen from a pulldown menu In the second step genotype terms can be assigned individually 2b or for the whole set of mice 2a Important when assigning genotypes individually ignore must be selected in the upper pulldown menu Pressing confirm genotypes leads to the next step 64 Logged in as admin log out Help MausDB DEMO W View mouse 3 mice in cart Home racks amp cages search find import reports settings empty cart Enter genotype phenotype information 2 step Please confirm mouse id lear sex cage genetic marker genotype phenotype 50005155 99 f 0296 abc 50005156 98 f 0296 abe Je 50005157 01 f o2s6 abc Figure 66 Step 2 Preview After final preview the genotype procedure can be started by pressing genotype Logged in as admin log out Help MausDB DEMO j Y View mouse 3 mice in cart Home racks amp cages search amp find import reports settings empty cart Enter genotype phenotype information 2 step Trying to enter update genotype information genetic marker genotype phenotype genotyping remark abc linserted genotype phenotype abc linserted genotype phenotype abc Genotyping done You may view genotyped mice here Figure 67 Step 3 Confirmation 5 7 How to change cost centre assignment for mice During the life of a mouse the cost centre that has been assi
81. ollowing steps are done as user admin 9 2 2 2 X server The MausDB R interface requires X to be installed Either choose X to be installed on your system at the very beginning e g by installing a desktop version or install the package kubuntu desktop which is quite an excess but will make sure X is running and set up properly If you choose a desktop ubuntu version that comes with the default Gnome Desktop this will do fine and you can skip the next step optional install kubuntu desktop sudo apt get install kubuntu desktop 2 2 3 ssh installation install the open ssh server and client sudo apt get install ssh if neccessary restart the ssh daemon sudo etc init d ssh restart After finishing this step login to the computer must be possible via ssh from a remote machine 2 2 4 Short introduction to apt Ubuntu Linux makes use of the package management system apt to install and manage software packages A package index is maintained on the local machine Using this index the system knows which packages are installed Prerequisites and dependencies between packages are known and apt resolves these dependencies or tells you about problems Local package index files are synchronised via the internet with so called repositories or sources In etc apt sources it can be defined which sources have to be used By including formerly commented sources the system can be expanded by other packages Search in
82. on as every cage is assigned to a rack and no errors are detected the next step button occurs at the very bottom which will lead to the next step Weaning 3 step 3 step check and confirm male pups mouse id eartag sex born line strain color cage rack comment remark Bi no female pups to wean Please check weaning data carefully If anything is wrong in the tables above go back to the previous step and make your changes wean or go back Figure 56 Step 3 Final preview A final preview is displayed Pressing wean will start the weaning transaction 59 Logged in as admin log out Help MausDB DEMO 0 mice in cart Home racks amp cages search amp find import reports settings Weaning 4 step 4 step wean male pups i a a eT mossa ba Im na fiseer anossa o gt n va ieox2007 no female pups to wean Print cage cards You may want to print new cage cards for all cages involved in the weaning Please use the links below e print card for cage 0283 Weaning successful You may want to see weaned litter here Add selected mice to cart Page generated on Tue May 15 14 20 03 2007 Figure 57 Step 4 Confirmation As the weaning has been completed mouse and cage IDs are available and displayed as clickable links Links to cage cards are displayed for every cage 60 5 5 How to import mice Mice that are not weaned within the facility that is
83. or total mice per line 4 13 2 Mouse strains genetic backgrounds overview In order to get an overview about all mouse strains genetic backgrounds n MausDB choose reports strain overview Mouse strains overview 4 mouse strains found alive strain name males females tot oe CE B CS7BL 6 4 CS7BL 6J BTNT al af o total living mice all strains 360 400 760 Figure 36 Mouse strains overview Multiple result pages can be browsed using the navigation links on top of the table Clickable strain names lead to strain specific detail views 46 4 13 3 Specific to Helmholtz Zentrum M nchen TEP report TEP s the German acronym for an an mal registration program The TEP system was developed on behalf of the Helmholtz Zentrum M nchen and is now licensed for use by Ascenion www ascenion de for the quantitative registration of laboratory animals of different species in an animal facility The TEP report module in MausDB provides an export of statistical information that can be used for import into the Helmholtz Zentrum M nchen TEP system The TEP report function produces a file in spreadsheet format xls It contains a matrix with columns representing different reasons for assigning a MausDB mouse ID Gmport weaning death reasons or different states a mouse can have breeding or experiment In the rows the numbers of animals are listed which belong to the corresponding category grouped by a calendar
84. our screen s all screens Page generated on Mon Apr 30 14 51 55 2007 Figure 9 User specific Home area Area 1 shows login information and the log out button as well as the cart symbol and cart information Area 2 is the main navigation bar Area 3 contains a help link and the mouse quickfinder form Area 4 can contain a list of user assigned litters Area 5 can contain a list of scheduled user tasks The next figure shows an example where litters and tasks are scheduled 28 Logged in as admin log out Help MausDB DEMO View mouse Home racks amp cages search amp find import reports settings Welcome MausDB Admin Litters to be weaned from your screen s litter ID project strain line born age cage males females commen i 06 04 2007 24 002 13 01 3 723 1002 14 0294 asc caH 07 04 2007 23 1002 09 0095 2 e m litter from mating 411 Projekt_ HIJ 4 B6 07 04 200 7 li caHep Fe1 12 04 2007 18 1001708 0107 litter from mating 366 Projekt_ C57BL 6 14 04 2007 6 01 08 01 litter from mating 42 4 001 06 034 Order lists for your screen s all screens order list name parameterset status mice Scheduled to week 19 2007 Monday 07 05 2007 x ABC FLP CON Mate 2007 05 07 admin Mate ordered 2 Scheduled to week 18 2007 Monday 30 04 2007 ABC 129 Sperm freeze 2007 04 30 admin Sperm freeze ordered 1 Page generated on Mon Apr 30 15
85. ouse strains genetie back crOunds Dove wann E E 46 4 13 3 Specific to Helmholtz Zentrum M nchen TEP report cc cssssssesseeeeeeeceeeeeeeeeeeaeseeeeeeees 47 4 13 4 Specific to Helmholtz Zentrum M nchen Versuchstiermeldung 0 en 47 4 13 5 SMADSMOU Lal Dunkel ee een ee 48 4 13 6 a OCCU MON ee a 48 5 DETAILED STEP BY STEP INSTRUCTIONS FOR COMMON TASKS 50 5 1 FLOW 10 Set upa mane 22 NER ISSN es rsnssunlerete 50 Sel Step Deunne minns partners seriell 50 adz Sep Doninte inane deals nis 51 3 43 281693 Conan Seesen 51 5 2 How toset up an embryo transfer needs 52 5 3 How toreport hieran aea aa EEN EAEE EE 55 5 4 How to wean litter or report litter 1085 te a 57 5 5 How 10 port MICE a RESTE NET 61 5 6 Howiogenoype MICO seisine eE E E L E 63 5 7 How to change cost centre assignment for MiCe sssssssssssssccccecccccccssssssccccccecoccccccccsssseccccceeceessssesssss 65 5 8 How to change experiment status Of MICEe eecccseceeeeoecosssssssescccccecccccccsssssssscccccccecccssssssssssssssccceceeesso 66 5 9 How to MOVE a mouse to another CAGE 000ss00sssnuuuenssssnsnnnunnnnsssssnnsnunnnnssssssssnunnnsssssssssssnnnssssssssssssnne 67 5 10 How to move a Cage to another rack 2 0sssssssssuunensssssssnnunnnnnsssnsnsnnnnnnssssnssnnnnnnssssssssssunnnsssssssssnsnnne 69 5 11 Howto Cullmicees are eu ee nnee 70 6 MAUSDB ADMINISTRATION 222 ae 71 6 1 Backup datapase isn acs ccecesstc
86. pfile sql that s it 3 2 Starting from scratch In case you install MausDB for the first time the following steps describe how to do that 3 2 1 Create the MySQL databases login to mysql as mysql root remember this is not the same root as system root mysql u root p lt password gt Attention no whitespace between p and the password create database mausdb and blob database mysql gt create database mausdb mysql gt create database mausdb_blobs create database user for MausDB means into same line mysql gt grant all on mausdb to lt user gt localhost a identified by lt password gt mysql gt grant all on mausdb_blobs to lt user gt localhost AY identified by lt password gt update privileges table mysql gt flush privileges quit the mysql command mode mysql gt quit 3 2 2 Creating database tables and functions using DDL scripts Create tables by running create table DDL script means into same line Create main MausDB tables mysql u lt user gt p lt password gt mausdb lt x home admin mausdb SOL setup_database create_tables_mausdb sql 20 Create MausDB blob database table mysql u lt user gt p lt password gt mausdb_blobs lt NEN home admin mausdb SOL setup_database create_tables_mausdb_blobs sql Some user defined functions mysql u lt user gt p lt password gt mausdb lt RN home admin mausdb SOL setup_database mr2string sql mysql u lt u
87. s admin log out Help M DB DEMO W k Cnm 0 mice in cart Home racks amp cages search amp find import reports settings Mating details oe previous next Parents of mating 335 role entered left mouse ID ear sex born death genotype strain line room rack cage parental status maing maang oO Gr Ze DEREN 106 Ip gt 6 oan ane NER 0 m 1 ee AN re ra fe 157 a o fi co ie y i Es ERSO Er I removed ce eee a E E ar FE Bi zu fH HE ii removed Add selected mice to cart Litters from mating 335 born weaned i Flv ar a reduced 1 litter litter 13 09 2006 los 10 2006 2 litter 03 11 2006 o7 11 2006 Details for mating mating 335 Mating type normal mating Mating name Mating start 21 08 2006 Mating end 07 11 2006 10 03 22 Strain gt tine HIJ B B6 Mating scheme Mating purpose Mating generation a assigned project Projekt_1 mating comment update mating comment Page generated on Tue May 8 11 45 20 2007 Figure 23 Mating details The top table contains the mating partners i e the parents The second table shows all litters produced in the course of the mating so far Clicking on the litter link in the leftmost column leads to the litter view see 4 7 5 Additional litters can be reported by clicking on the report new litter button The bottom table shows mating de
88. s in var maus_connect DB_connect pm sudo nano var maus_connect DB_connect pm enter suitable settings username amp password adapt MausDB config files t sudo nano usr lib cgi bin mausdb config rc enter suitable settings 2 3 5 Create the directories for the backup system Some directories must be created for the backup system cd home admin mkdir home admin backup mkdir home admin backup daten mkdir home admin backup daten lt yourfacility gt mkdir home admin backup logs mkdir home admin backup logs lt yourfacility gt 2 3 6 Installation of the backup script copy backup script and set appropriate ownerships cd home admin backup cp home admin mausdb services backup pl CO sudo chown R admin admin backup 18 adapt settings in backup pl according to your system and paths sudo nano backup backup pl Although this should be rather self explanatory some help and explanation All settings are stored in a 2 dimensional global hash named backup_data The first numeric key describes the database to be backed up the second text key describes the specific setting for this database Sections Sbackup_data O global settings for all databases Sbackup_data l settings for first database Sbackup_data 2 settings for second database Below this settings block there are some if entries In order to include a database into the backup script you need to generate a s
89. second table row from a pulldown menu Alternatively a new strain can be defined by choosing new strain in the pulldown menu and entering a new strain in the input field The same procedures applies for mouse line selection in the third table row In the following rows additional embryo transfer information can be given Defining a project will remember project assigned users about litter weaning Other fields can be optionally filled by users Pressing the setup transfer button will finally set up the embryo transfer and present a confirmation page see below 53 Logged in as admin log out Help MausDB DEMO z ei VW View mouse 2 mice in cart Home racks amp cages search amp find import reports settings empty cart New mating trying to set up new mating type embryo transfer in the database Checking mating partners e checking female mouse 50003930 for mating ok Moving mice mouse 50003930 stays in cage 0005 Setting up new mating Mating type embryo transfer successfully set up in cage 0005 print cage card See mating 494 for details Page generated on Fri May 11 10 44 10 2007 Figure 47 Step 3 Confirmation Clickable links for mating ID and mating cage are displayed Logged in as admin log out MausDB DEMO Y View mouse 2 mice in cart Home racks amp cages search amp find import reports settings empty cart Mating details previous next Parents
90. see 4 7 4 and ancestors show ancestors see 4 7 3 are given For imported mice a link to the respective import see 0 is displayed The Breeding record table shows every mating in which the current mouse is was mating partner The Genotype information panel shows all genotype data for the current mouse Properties e g foreign IDs for imported mice and attached files are listed if available 34 By following the edit details link in the previous figure the following page 1s displayed Edit mouse details Details for mouse 50005137 15nnns5137 current 3 new cu i e current n ayy d afii ew e update earmark update sex update color Ino comments for this mouse update comment back to mouse details Page generated on Tue May 8 10 20 09 2007 Figure 19 Edit mouse details Some individual mouse properties eartag sex color and comment can be changed here Other properties like for example date of birth not only affect an individual mouse but a whole litter and therefore must be changed by a trained administrator on the SQL level 4 7 Some more informational views 4 7 1 Cage history of a mouse Sometimes it is not only important to know where a mouse is currently located but also in which rack and cage a mouse was housed in the past together with which cage mates This kind of detailed cage history can be viewed with MausDB easily Logged in as admin log out Help
91. ser gt p lt password gt mausdb z N home admin mausdb SOL setup_database get_number_of_cagemates sql mysql u lt user gt p lt password gt mausdb lt EN home admin mausdb SQL setup_database get_simple_value_for_mouse_p_ps sql mysql u lt user gt p lt password gt mausdb lt NEN home admin mausdb SOL setup_database mice genotypes sql Now all tables are defined but empty Some initial values need to be in the database in order to start This is described in the following steps 3 2 3 Load initial settings into database Some initial and essential settings are set in the following steps by loading pre filled tables into the database means into same line Master data for days mysql u lt user gt p lt password gt mausdb lt KR home admin mausdb SOL setup_database days sql Master data for settings mysql u lt user gt p lt password gt mausdb lt home admin mausdb SOL setup_database settings sql Master data for death_reasons mysql u lt user gt p lt password gt mausdb lt home admin mausdb SOL setup_database death_reasons sql initial admin user account username admin password mausdb mysql u lt user gt p lt password gt mausdb lt home admin mausdb SOL setup_database initial_admin_account sql initial mylocks mysql u lt user gt p lt password gt mausdb lt home admin mausdb SOL setup_database mylocks sql optional examples for phenotype and routine task work
92. sing Report litter Litters from mating 492 born weaned wens mn P reduced comment 1 jitter 11 05 2007 not yet weaned delete wean J 0 Details for mating mating 492 Figure 52 Step 3 Confirmation After pressing Report litter the litter has been added to the litters table in the current mating view Clicking on the litter column 1 will lead to the litter details page see 4 7 5 Using the links in the third column the litter can be deleted or weaned respectively 56 5 4 How to wean litter or report litter loss As soon litter has been reported to MausDB it can be weaned The weaning procedure either starts from the litters table in the mating view see Figure 52 or from the litters table in the Home area see Figure 10 In either case a click on the weaning link will start the weaning dialog The weaning procedure in MausDB includes the generation of mouse IDs for all weaned mice eartag assignment and rack cage allocation of these mice In the following example a litter with 3 males is weaned Logged in as admin log out Help MausDB DEMO te Y View mouse 2 mice in cart Home racks amp cages search amp find import reports settings empty cart Litter details 2 1 Litter from mating 489 weaning overview birth date ig 04 2007 7 comment update litter comment 1 litter from mating 489 parents EA father 50004622
93. t genotype flags e g need to be defined As admin choose settings new genotype 25 Logged in as admin log out Help MausDB DEMO y View mouse 0 mice in cart Home racks amp cages search amp find import reports settings Create anew genotype Genotype info laenotype Please enter the new genotype define new genatype Page generated on Wed May 2 11 02 40 2007 Figure 7 Define a genoype something like wildtype can be entered 3 4 8 Configuring email address es for admin user s In some cases MausDB automatically sends email notifications to defined recipients e g upon the generation of new mouse lines via the web user interface To this end email addresses for notification recipients need to be defined in the database Start the mysql console mysql u lt user gt p lt password gt mausdb Define email addresses es mysql gt update settings set setting_value_text lt email address gt where setting_item admin_mail 26 4 Working with MausDB for all users 4 1 Some basic concepts There are some basic concepts that you need to understand before working with MausDB At least it makes working with MausDB much easier 4 1 1 Everything has an ID Everything needs to have an ID in databases This is also true for MausDB since MausDB is a database application Every mouse has an 8 digit numeric mouse ID
94. tails for example mating start mating end line offspring line comment 37 4 7 5 Litter view In the litter view parents and littermates of an individual litter are shown together with litter details for example date of b rth date of weaning and comment Logged in as admin log out Help MausDB DEMO y C 67773 0 mice in cart Home racks amp cages search amp find import reports settings Litter details 1 Litter from mating 335 weaning overview alive dead re duced io a eee date total male fem ale total male female total wh 13 09 2006 09 10 2006 9 4 FE fo L EHE 14 comment update litter comment 1 litter from mating 335 parents ID rote mouse hekau ber E E father sooosu02 oz m 13 05 20 2 E frower somsa oe feae z006 Add selected mice to cart e death genotype strain line roomzrack cage paast v o ko 11 2006 a 1 Litter from mating 335 littermates a death genotype strain line room rack cage gt Hu e 86 gt hosse Ee HIJ B B6 001 01 0 JM ea HIJ B B6 017 ES a f3 09 2006 ft 13 09 2006 if 13 09 2006 fes 09 2006 means that this mouse was is used as parent in a mating Add selected mice to cart HIJ B B6 1001 01 0174 wu 237 s a73 _ os 03 2 Ea BE 2 HIJ B B6 1001 01 000 Fee EEE EZ s feeos zo07 v _
95. tem root account 11 2 2 11 Installation of mailx and postfix Install the mail system by typing sudo apt get install mailx Choose Internet Site in the following postfix configuration ALS OO 2 2 12 Installation of ntpdate Install the ntpdate client to synchronize system time to time servers sudo apt get install ntpdate 2 2 13 maybe required set a password for the Mysql root user There is a mysql admin user named root which is comparable to the user sa in other DBMSs Attention mysql root is different from the linux root user Set the password for mysql root may be skipped if root password has been set at mysql installation sudo mysqladmin u root password lt new password gt lt new password gt 1s to be replaced by the new password 2 2 14 Install some packages neccessary for CPAN In order to be able to install Perl modules via CPAN some additional packages must be installed by typing suoo ape ger InsEaLlt nerep sudo apt get install Lynx sudo apt get install unzip sudo apt get install make sudo apt get install gcc Se SE OSE SE FE 2 2 15 optional Create a directory for the mysql binary logs Ideally the binary logs directory should be on a separate hard disk and for this reason independent from the one which hosts the database You also can leave everything on default and skip this step If mountpoint s separated from mountpoint var e create a directory for the binary logs
96. ther with genotype information see Fig 22 In case of very wide ancestor trees a link more is given which can be followed to use the particular mouse as the root of a new ancestor tree Ancestors of mouse 50003923 father 50000781 father YA 50000790 y hij mother 50000782 father y hig mother imported 50003102 L his y Ai father father imported 50000781 father imported mother imported father imported mother Y mother imported 50000792 L y Aig mother 50000782 y Ai father imported male 50003923 ee EEE hij father father imported 50000781 father 41 mother imported 50000730 y hij mother 50000782 mother imported father imported mother hii mother imported 50003106 _ y hij father father imported 50000781 mother Y W nother imported 50000792 ly hij mot hex 500007832 iy hay father imported mother imported Figure 22 Ancestor table The mouse for which the ancestor table was called is displayed on the left Next to it on the right side father and mother ID along with genotype information are shown and so on 36 4 7 4 Mating details view In the mating details view mating partners and litters of a defined mating are shown in an overview How to set up a mating in MausDB is described step by step in chapter 5 1 Logged in a
97. ts Phenotyping data is organized in pre definable Parameters within MausDB Sets of parameters that result from an assay can be grouped organized in so called Parametersets These can be viewed and defined via the user interface reports parameters reports parametersets Example parameters and parametersets can be generated using the script parametersets sql that is part of the download repository means into same line mysql u lt user gt p lt password gt mausdb WA home admin mausdb SOL setup_database parameters sql Parametersets overview create new parameterset Fy parameterset description screen project klass lis active l records a example set example parameterset SMcI 1 y oO 2 mate mate amer 4 sml Page generated on Tue Mar 30 16 56 08 2010 Figure 29 Parametersets overview Two example parametersets are shown Parameterset overview example_set overall min mean max 1 Excel upload configuration mouse ID column ate time column you may update this column 2 Metadata definitions parameter set example_set No metadata definitions found for this parameter set add metadata definition 3 Parameters belonging to parameter set example_set parameterset settings updated Excel upload move name short name description nit metadata type category default value normal range increment increment unit required se ee Ex

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