PDF - Matrix Science
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1. 36 Sources of Information Using Mascot Server The HTML help pages Mascot Server installation configuration and troubleshooting Installation amp Setup Manual e Support pages on www matrixscience com Using Mascot Daemon Online help F1 Using Mascot Distiller Online help F1 Anything not answered by the above e supportematrixscience com MASCOT Administration amp Configuration 2007 2014 matrix Science SCR Finally a reminder of where you can find technical information about Mascot 372. amp Configuration 2007 2014 matrix Science NC There are potential issues with older legacy applications that interface with Mascot but don t have code to support the security system Since session ids are saved as cookies and since most Windows applications that access web sites use Microsoft Internet Explorer libraries it may be sufficient just to login from an Internet Explorer browser window before starting the application Alternatively you can use one of the special user types 15 Example 3 party applications Computer name IP address e Never have to log in from that computer e Use the computer name IP address as the name Agent string e Can determine the agent string from the web server logs e Not secure because someone could create another app to use this agent string Web server authentication MASCOT Administration amp Configuration 2007 2014 matrix Science CR These methods are less secure than a password protected login but ensure that all applications are able to connect somehow 16 Mascot Security general tips e Plan carefully before implementation e Login as admin to perform admin tasks e Enabling Mascot security doesn t stop your server from being hacked e Moving Mascot to another computer Just copy over user xml eroup xml and security options xml MASCOT Administration amp Configuration 2007 2014 matrix Science i NC I can t stress enough tha
3. are available Mascot users can be given the privilege to submit searches under other user names This is particularly useful in a core lab when customers only have privileges to see their own search results so the instrument operator needs to submit their searches under individual customer log in names The security task is For Mascot Daemon allow spoofing of another user 13 Example Daemon amp Distiller e Mascot Daemon ogg File Edit Help Status Event Log Task Etor Parameter Editor Drag and drop data files into the area belcw or click on Add e Pute export External processes No totew uo required b i r Delete ne r sa h zb f zl F home Merge MSMS files inte aingle search MASCOT Administration amp Configuration 2007 2014 matrix Science NC If this has been enabled for the user who is running Mascot Daemon then a drop down list of other Mascot user names will be enabled on the Task Editor tab 14 Example 3 party applications Older applications that submit searches to Mascot won t have their own login Try logging in using Internet Explorer before running the application cookies Use one of the special user types Email address User type User authenticated using web server Multipl Standard Mascot user shift Computer name P address Agent string User authenticated using web server Account enabled K Cancel MASCOT Administration
4. t copy this across your job numbers will start all over and you ll have to sort the search log by descending start time to locate the most recent searches Some people import the search log into a database application so as to make it easier to search or filter especially if it gets very large 29 Log files database status Bae id inani d haa pem Con 2g MASCOT search status page Verso 240 Haia Creer Ei hkupr irgi LOC X P HI Mi Y Logged m as Jaha Caneel pcos eg Soden and VO procmtsord 0 pearcbers MASCOT Administration amp Configuration 2007 2014 matrix Science NC The database status page has links to many of the log files mentioned earlier This 1s the starting point for troubleshooting problems especially those connected with database updates When Mascot Monitor first starts there 1s a single entry per database Once a database has been updated there are two entries one for the old file and one for the new We need this double view because of the way databases can be updated in the background without interrupting searches During database exchange while the new file is compressed and tested searches can still be submitted to run against the old file Once the new file is ready all new searches are run against the new file So on a busy server there may be a period when you have searches running against both the old and new files As soon as the last search on the old file has completed the
5. Administration amp Configuration MATRIX SCIENCE Installation amp Setup L Muncet search enne jP x Mascot Daemon Mascot Documentation Setup A Invtallatian ome Heleate Notes T MASCOT Administration amp Configuration 2007 2014 matrix Science CR The Mascot Installation amp Setup manual 1s linked from your local Mascot home page If you need detailed information on any aspect of Mascot installation or configuration this 1s the place to look Installation amp Setup PFFF lt eo p omm dii Colabora l wl PF sg B fem SD Commen ad Dente WHFS 39 es ranog oe a il lf the executable string in ExecAfterSearch includes Percolator Exe Flags this ps exparided ns follows where PercolatorExeFlars t the value of PercolatorExeFlags in maseot dat ote that D 14 will be suppressed automatically if PercolatorUseRT is set toO or if the peak list that has beer searched doesnt contain any retention times Paths to executables and any patha included as arguments whould use forward Hashes and should not mclude spaces FeatureTablelength 3 lf a riacleie acid sequence is longer than 30000 bases the protein view report will automatically switch to feature table mode and output the matches as a GenBank feature table The threshold for etching to feature table mede can be altered umng the parameter Feature TableLength in the ptiona section of masot dat or by appending featuretableblength X to t
6. T Administration amp Configuration 2007 2014 matrix Science NC similarly for Enzymes and Instruments The other sections Quantitation Database Manager and Security have been touched on in earlier presentations 26 Configuration Editor wd tlt Rie ot Configuration Editor Edit Mascot Options s T m H FETT 1 lair GeIpne MATRIX MASCOT Administration amp Configuration 22007 2014 Matrix Science SCIENCE The Configuration Options section deals with various global settings stored in mascot dat Remember that all the sections of mascot dat that deal with sequence database configuration may be re written at any time by Database Manager If you ve been in the habit of editing mascot dat in a text editor only the Options and Cluster sections can be modified safely unless you decide never to use Database Manager There are two configuration files that are missing from the configuration editor Taxonomy categories taxonomy and Cluster geometry nodelist txt If you need to make changes to these you still have to use a text editor You can find full details of the file formats in the manual 27 Log Files Troubleshooting The files in the logs directory are the first place to look if there is a problem Installation install log Windows only e General errors errorlog txt e Database update utility ftp log txt e Mascot Monitor events monitor log Security events security log e Cluster bootstrapping l
7. checkboxes determine whether a column is shown or hidden The two hidden columns are Ti for title and In for intermediate file This 1s a hyperlink to display the raw mascot result file but you can only see the first two characters of the file name which are The hyperlink in the first column displays the formatted result report You can set the number of lines to display and whether to start at the beginning or end of the file You can also filter the display by entering text into the edit boxes For example your user name or a word from the search title If you have split the search log into sections then you can choose which file to display by entering the path 32 Log Files Troubleshooting Other useful files Database compression lt database gt current lt database gt errors Database taxonomy lt database gt current lt database gt NoTaxonomyMatch txt Database statistics lt database gt current lt database gt stats e Web server access and error logs System event or message log MASCOT Administration amp Configuration 2007 2014 matrix Science EC The first three files are most easily viewed using the links in database status Sometimes there will be nothing in the Mascot logs because the problem is external to Mascot Sometimes it can be useful to look at the web server logs or even the operating system logs The Windows Event Viewer control panel administrative tools allows you
8. guration 2007 2014 Matrix Science CR In a core lab you may want a group that enables customers to view their results In this case only give them rights to perform these tasks You must allow all fasta databases to be searched otherwise they won t be able to view reports However they can t perform PMF or MS MS searches because this task 1s missing 1 Example Core Lab Customer MATRIX SCIENCE JE eri maa UC MASCOT Search Result avaro eame uem He pub peu uia is tek pees sd hag ijy erin lasmily Seeman Z2 Prete Passes 1 16 out cl 9490 MASCOT Administration amp Configuration 2007 2014 matrix Science CR A group member will be able to view the search log see their results but when they try to do a repeat search access 1s denied 12 Example Daemon amp Distiller oo ee ae 1 p Mascot Security edit group Daemons E e 4 s Y m H FETT 1 lair GeIpne MATRIX MASCOT Administration amp Configuration 22007 2014 Matrix Science SCIENCE Client software like Mascot Distiller and Mascot Daemon requires special privileges The Mascot Daemon user must have the security token Mascot Daemon is allowed to submit searches The default daemons group settings shown here are appropriate for either a Daemon or Distiller client View config files 1s required because both clients need to retrieve configuration information from the server like a list of the databases that
9. he proteim view LRL where X ia the mius q io F FeatureTableMi Ee By default only matches with significant scores p 0 04 are output A different wore threshold can be specified using the parameter lFFeatureTableXMinScore in the U ptiona section of masoet dat or by appending featuretableminscore X to the protein view LRL where X ia the score threabold MASCOT Administration amp Configuration 2007 2014 matrix Science CR This is an administrator s manual not a user manual You won t find much relating to how to submit a search or how to interpret the results User help is in the Mascot HTML pages Installation amp Setup Mascot Security Configuration Editor eLog Files Cluster mode MASCOT Administration amp Configuration 2007 2014 matrix Science SCR These are the topics we will cover in this presentation Mascot Security Examples of how Mascot security can be used e Ordinary users can browse configuration files and status screens but not make changes Certain sequence databases are private to a group of users e Limit some users to one search at a time while others can run many searches simultaneously e Limit the length of searches from a particular group to 1 hour Prevent certain users submitting no enzyme searches Let customers view the results of searches run for them without being able to submit searches themselves MASCOT Administration amp C
10. ion 1s confidential or because you are just experimenting If so use the Modifications section of the configuration editor 22 Configuration Editor View Modification Piperidine MASCOT Administration amp Configuration 2007 2014 matrix Science CR The user interface is fairly self explanatory and help is displayed for each field when you mouse over the label If the modification is from the downloaded unimod xml file and you want to make changes click on the Make editable link 25 Configuration Editor Edit Modification Piperidine re 2 ien Il BE E Daea b gi piani 315 MASCOT Administration amp Configuration 2007 2014 matrix Science CR All aspects of the modification become editable If you want to see the differences between the original Unimod entry and the local entry choose Show differences If you want to discard your changes choose Revert to Unimod 24 Configuration Editor ay eS lp eee Q D wipe Mascot Configuration Modifications ee Viri y Tie 4 HA Dm ee ee MARI 2ONB MU imr Pe i jape imak 270240 20D 2002313704 MASCOT Administration amp Configuration 2007 2014 matrix Science SCR The top level page allows you to filter the listing Here we have checked the box to show only local definitions 25 Configuration Editor Mascot Configuration Enzymes MASCO
11. n 2007 2014 Matrix Science CR You can edit these files in a text editor but it is easier and safer to use the browser based Configuration Editor The first three entries are interfaces to different sections of unimod xml 19 Configuration Editor Mascot Configuration Symbols rae laces Tyrki Mara omn wie jl ETES Lica i 1538 Me 13 18 pm ages jf mmus Eg o mo FPREECRRTCOGHHIEEUUC MASCOT Administration amp Configuration 2007 2014 matrix Science NC You may need to add or edit an element or an amino acid but its fairly unlikely QO E m e JU mh yr fem e ILG EL Dua P let pip id UNIMOD Lire Sears h lar pF MASCOT Administration amp Configuration 2007 2014 matrix Science EC The modifications file unimod xml is an XML representation of a public database called Unimod This 1s the interface to the public database From time to time you should update your local file by downloading the latest file using the links in the Unimod help Zi Configuration Editor 2 ies de c C Oop Mascot Configuration Modifications Corolla di indt Vds d MASCOT Administration amp Configuration 2007 2014 matrix Science NC If you need to add a new modification that will be of interest to others it s best to add it to the public Unimod database so that the information is available to all Mascot users If you want to create a local definition because the modificat
12. ng advantage for a single spectrum Search results are returned to the master which merges them and writes the result file to disk All master node communication is via TCP IP This uses simple socket based communication A parallel operating system is not required Configuration and program files are distributed and updated automatically from the Master node so the cluster behaves and looks like a single server Sometimes we are asked about running Mascot on a general purpose server farm that 1s being used for other applications For standard PC hardware the cost of the Mascot licence is greater than that of the hardware For a given capacity the lowest cost route will always be a minimum number of licences on dedicated hardware If you want to run Mascot on machines that are part of a larger cluster best to partition off a number of nodes either for exclusive Mascot use or where Mascot has absolute priority over other processes Mascot cluster nodes cannot be dynamic because of the size of the database files The time taken to move these files between machines or even just in and out of memory would always be unacceptable 35 Cluster mode Mani inani d ol pone LE ramTlYy Sy IS ees I us mw uq mus EIBEJ SUFTWHE Im EGBE TE TE BOR iar IO120710 fasta Patkname usr lsewl maseor i 4 0 H sequence MCBIns curt tnt HE Inr 20020710 EEES y Ca TE the ry E T i ud Wed Jul i11 i5 14 44 F mearchesm 0 s TES DPeqe
13. oad node log Unix only Cluster communication ipc log MASCOT Administration amp Configuration 2007 2014 matrix Science CR The log files are the first place to look if there is a problem Most of these files can be accessed from a browser via links in the database status utility which we ll come to in a minute 28 Log files searches log e May need to split roll over the log if it gets very large e Can be recreated using ms makesearchlog exe e If you move Mascot to a new machine transfer searches log and mascot job along with the search results files e Tab separated values easily transferred to spreadsheet or relational database MASCOT Administration amp Configuration 2007 2014 Matrix Science CR Every Mascot search adds a new line to the searches log If the server is busy the log files can get very large For most of the logs you ll probably want to delete the file from time to time The searches log 1s different and you ll probably want to keep all entries indefinitely Best idea is to rename the file periodically For example searches log 20060301 The system will then create a new one automatically If the search log is accidentally damaged a new one can be created by scanning all the result files on the disk If you move Mascot to a new machine you ll probably want to transfer or rebuild searches log The other important file 1s mascot job which contains the next job number If you don
14. old database can be taken out of use Mascot monitor takes care of all of this automatically 30 Log files database status E cca LET IM EM Monon ine ined Caplio Fm EL Yew frein fo Hep O OD HBG pme onaf montay amp inp cada mae oil Jac mm aun ama a for rr m eem KO TCR Se Dat bata a uet t T Mascot Job status Job 2696 Database HCBI5E Job Mumber E 2696 Process ID 1996 0 Cr RB Pillar D leafl mul ch Search tit Le 1 A fee peptides from an LCES run Percent complete Z Intermed file i L datali0060201 FDOS 69d dat Start time i Wed Feb OL 11 20 37 ZDOR End time Searching time 0 Upload time Query prep time Whole process time Job status I parching i Priority curresBk valust D Change this by IP address 192 168 8 1325 Type of arch NIS Enzyme i Tes CPO utilisation i U Mo requests E11 Pause Papis MASCOT Administration amp Configuration 2007 2014 matrix Science EN CR You can drill down from the database status page to a list of searches for each database and then down to the details of an individual search as shown here If necessary you can kill or pause a search from this page or change its priority Log files search log viewer MASCOT Administration amp Configuration 2007 2014 matrix Science CR This 1s the search log viewer You can sort on any of the columns using the radio buttons and then pressing Sort filter The
15. onfiguration 2007 2014 Matrix Science CR Mascot security 1s not a substitute for a firewall It won t stop your server being hacked or infected by a virus It is a way of managing and allocating the Mascot Server resources Mascot Security enable disable EE MATRIX SCIENCE C slnet pub SAASCoTsbhinsenable The password For the admin account hi TI will be required to change it a 2 next login Lisi net pub SAAS COTS bain gt 2007 2014 Matrbr Scienc MATRIX ZU 2t Matrix Science SC ENCE MASCOT Administration amp Configuration When Mascot is first installed Mascot security is disabled So if you try to log in you will see this message To enable security open a command prompt or a shell on the Mascot server and change to the mascot bin directory Type enable security pl or enable security pl if Linux This takes a few seconds If you forget the administrator password it can always be reset to admin by running this script again Mascot Security administration ae at khim L Mascot Security Administration haty In iodrafi TAE uA MATRIX MASCOT Administration amp Configuration 2007 2014 Marix Science SCIENCE All security configuration is browser based The top level page of the security administration utility looks like this There is a list of users a list of groups and a few options If you hold the mouse over any of the blue text help will appear at the bottom of
16. se privileges by being members of one or more groups Mascot Security tasks For example e Allow PMF search e Allow MS MS search Maximum number of queries e Can view the search log e Can search specific databases Can view other peoples results MASCOT Administration amp Configuration 2007 2014 matrix Science CR There are 30 different tasks that members of a group can be allowed to perform for example Mascot Security add user Mascot Security Administration Add user MA SCOT z Administration amp Configuration 22007 2014 Matrix Science A Adding a new user is very simple The Administrator must enter a username and password and it is usually a good idea to force the user to enter a new password when they first login Enter their full name and email address The user will be able to change this I ll return to the choice of user types later most users should just be standard Mascot users Make sure that the account 1s enabled and then select one or more groups for the user to belong to 10 Example Core Lab Customer If you don t want the customers to be able to do any searches but just view the results then just give them the access to tasks SEARCH Allow all fasta databases to be searched VIEW See search results from other people in your own group VIEW Allow user to view the search log ADMIN Allow use of Database Status application MASCOT Administration amp Confi
17. sst to mem map TIS Pequeest uneap MO Nem locked H 1 Current TES hr eeds EIcE TpIDifOMe LAE il 1 114 18 P searches 0 st to mem map TES Request unmap HO fem Locked NO urrent TIS Family lfwmr local m amp scot Z 4 0 tA mepurnce Tiras Afcurpest ITEGI FANRtA m Pa L L j z B mame ETE current T 1 pr tsi Prete ine fart Pas Bric ZuaSLELILE ime Wed Jui 11 17 20 13 B searches d TES Beqerst to mem map TES Request umeap N fem Locked NO Mite of threads Current TIS Chaster Nodes eie E Adios ON Responding Tiyatro Memory espe Disk spate aded 10253111 fL OK D B0 fee 1S 1009 ee PE 1594 tee food 1024112 Lej og f 1S 100 tee 19 fee beddi 025113 Lem ok Osmse 100 se 19 tee fede 1023114 Le G ok f 1S 100 tree 9 197 See sede 1025115 Lem Og Meriter 100 bee P 20 hee MASCOT Administration amp Configuration 2007 2014 matrix Science If you have a Mascot cluster it is almost as easy to administer as a single machine Everything is reported and controlled through the master node The Cluster Nodes table provides a an overview of the search nodes smiley faces or green unhappy faces If you need a closer look at one of the search nodes follow the links to view the search node log files Fumily gt Furp loc amp l m amp scot I 4 0 4 rrpence rice protseome current fnsta Fathima 9 usr loc amp l mascot 4 0 4meqerncom rice protsecem curtrent ri
18. t you should plan what you intend to do before you start Think carefully about what groups you want to create As any Unix administrator will tell you it s always best to separate your administration and user tasks However we can t force you but that is why the default admin user cannot submit searches It is very important to understand that Mascot security does not provide protection against a malicious hacker Hackers don t attack a server through Mascot they ve probably never heard of Mascot They attack through weaknesses in the operating system and through flaws in well known applications like the web server It is still essential to have a dedicated firewall between the Mascot server and the Internet 17 Configuration Editor Almost everything in Mascot is configured using text files in the config directory e General settings mascot dat Masses and modifications unimod xml Enzymes enzymes MS MS ions series fraementation rules Taxonomy categories taxonomy e Cluster geometry nodelist txt Security eroup xml user xml security options xml security tasks xml MASCOT Administration amp Configuration 2007 2014 matrix Science CR Almost everything in Mascot is configured using these text files in the config directory The syntax for each of these files 1s described in the manual 18 Configuration Editor Mascot Configuration MA SCOT s Adm in is tra tion amp Con figura tio
19. the screen The options shown on this page are global options which apply to all users Reference You can t disable security from here it has to be done on the server using the disable security command The session timeout is in seconds After this period of inactivity the user will be required to login again The password expiry time is in days After this period of time the user will be required to enter a new password Set to 0 to allow passwords to be permanent Any new password must be at least this length Session cookies are automatically destroyed when the browser is closed With some browsers session cookies are not shared when a new instance of the browser is opened which might mean that a user has to login again for each new window opened If verify the IP address is set then any request to perform a privileged action will compare the IP address that the request is coming from with the one originally used to login Logging level should normally be left at 3 Mascot Security role based Users Groups Login name Name e Password password List of members expiry e List of allowed tasks Full name email address Account enabled disabled Member of one or more groups MASCOT Administration amp Configuration 2007 2014 matrix Science CR Mascot security is role based This means that privileges known as tasks are assigned to groups not individual users Users gain the
20. to browse Windows system messages 33 Cluster mode lb External Intranet Fr TCP P S TCPIP Mascot Cluster Topology Mascot node 3 MASCOT Administration amp Configuration 2007 2014 matrix Science SCR Just a few words about Mascot cluster mode Mascot supports cluster operation using a Beowulf like topology Mascot supports cluster mode as standard whenever the licence is for 4 CPU s or more You just have to hook up an appropriate number of PC s on a local LAN 34 Cluster mode Every search is distributed to all the cluster nodes Each node searches a portion of the sequence database Get the parallel processing advantage for a single spectrum Search results are returned to the master which merges them and writes the result file to disk All master node communication is via TCP IP Simple socket based communication e No parallel operating system required Configuration and program files are distributed and updated automatically from the Master node A cluster behaves and looks like a single server Need dedicated or partitioned hardware Cannot allocate machines dynamically General purpose server farm usually not cost effective MASCOT Administration amp Configuration 20072014 matrix Science CR In cluster mode every search 1s distributed to all the cluster nodes and each node searches a portion of the sequence database This means that you get the parallel processi
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