inTB - User Manual - Computational Genomics Laboratory
Contents
1. 302. Create a MySQL account for a user specific for intb 4 Configure inTB to use this intb user var django inTB inTBsite settings py 5 Change SECRET KRY on settings py same as point 4 according to https docs djangoproject com en dev ref settings secret key 4 4 Changing the system 26 CHAPTER FIVE TROUBLESHOOTING Table 5 1 Local installation problems Problem Solution The message Minimize this black window is displayed in VirtualBox but cannot access inTB after installation Check that your firewall allows local connections Try disabling it temporarily On MacOS run sudo ipfw flush The message Kernel panic is displayed in VirtualBox Restart VirtualBox If it happens again and you are using the 64bits image use the 32bits image instead You can t find the mouse and the keyboard is locked in VirtualBox Press the Right Ctrl key on Windows and Linux or the Left Cmd key on MacOS on your keyboard to release the mouse and keyboard I want more follow up options alternatives In order to add other follow up options you need to use the Advanced access to database and insert the desired option in the table entry_db Additionally the column order must match the temporal order of different follow ups 27 CHAPTER SIX GLOSSARY Clinical form Different symptoms which reflect the type of tuberculosis infection e g Pul monary Meningitis
3. Episode Record of infection One patient may have more than one episode if infection reoc curs by the same or a different species strain H37RV A strain of M tuberculosis commonly used as reference MIRU VNTR Mycobacterial Interspersed Repetitive Units Variable Number Tandem Re peat a method by which you can count the number of times a sequence is repeated in a given set of locus RFLP Restriction fragment length polymorphism a method based on the restriction pattern of a predefined set of enzymes Sample Biological sample which is then analyzed with different methods More than one sample may be collected for a single episode SNP Single Nucleotide Polymorphism identifying single nucleotide variations scattered across the genome Spoligotype A method which detects presence or absence of 43 unique spacers between re peats in a specific locus VirtualBox An application which allows running different operating systems as if they were independent applications VirtualBox image A full operating system including inTB and all required dependencies Once installed one click and you are ready to go User Manual The present document zip tar package A package which include all files you need for deployment except depen dencies recommended only for advanced users and system administrators Hardware virtualization A technology present in most recent processors which allows vir tualizing an operating system In practice this mea
4. of the hospital Submit Cancel Search for a term in Bio and Medical ontologies here Figure 3 8 Adding new option Once confirmed the new option will be automatically selected and will be available in the future 3 3 Adding data 22 inTB User Manual Release 1 0 Selecting dates Dates can be selected by clicking on the small blue calendar icon or by typing in the date in the correct format If the blue calendar is clicked a widget will be displayed where you can select the date Date of diagnosis 5 Fo YYY MM_D Appointment date M ay 20 1 3 Today Symptoms date Tuberculosis treatment start date Radiology 3 Select date Bb e L a SE otc bna arn bs Figure 3 9 Picking a date using the widget 3 3 2 Single entry Using the forms L Select type of data to INSERT o Patient information m Clinical Socio demographic Contact Follow up o Infection information m Resistance Molecular 2 Select type of data to UPDATE o Patient information m Clinical Socio demographic Contact Follow up o Infection information m Resistance Molecular Figure 3 10 Inserting Editing data Information is divided into Patient and Infection information The former includes clinical and socio demographic information as well as contacts and follow up records The latter includes molecular information about any collected samples While adding patient data using the forms th
5. on your disks with the content of the VirtualBox disk It s easier because all dependencies are already included Detailed instructions under Reusing VirtualBox content 2 Use the inTB Package found on the Download section of the inTB website Use this option if you want to install inTB without replacing the system You will have to setup all dependencies manually Detailed instructions under Installing from source inTB User Manual Release 1 0 2 2 VirtualBox Setup VirtualBox images are the simplest way to run your own test version of inTB but first you need to Installing VirtualBox 2 2 1 Installing VirtualBox VirtualBox platform packages The binaries are released under the terms of the GPL version 2 o VirtualBox 4 2 12 for Windows hosts gt 86 amd64 o VirtualBox 4 2 12 for OS X hosts x86 amd64 VirtualBox 4 2 12 for Linux hosts o VirtualBox 4 2 12 for Solaris hosts 86 amd64 Figure 2 1 Download links on VirtualBox s download page In order to start you need to download and install the VirtualBox application You can do it by visiting http www virtualbox org and downloading the VirtualBox platform package matching your system Software Installation N The software you are installing has not passed Windows Logo testing to verify its compatibility with Windows XP Tell me why P led i Continuma your eee this toftwaro may impak or destabilize the correct operation of your system either i
6. under Advanced Topics If this is the first time you are using VirtualBox you will be presented with a few messages They explain certain aspects of how VirtualBox works If you are done with them you can select Don t show this message again and press OK If your firewall prompts about VirtualBox trying to access the network please allow it or you may not be able to work with inTB inTB doesn t require access to external resources but requires that port 8181 is reserved in order to run locally 2 2 VirtualBox Setup 10 inTB User Manual Release 1 0 2 2 5 Acessing inTB Now that you have everything ready and VirtualBox running the black window is visible and it displays login details you can use inTB Machine View Devices Help L 13 8873321 piix4_smbus 0000 00 07 0 SMBus base address uninitialized upgr de BIOS or use force_addr 0xaddr Ubuntu 10 04 4 LTS inTB tty1 Login details root Password root inimize this black window and use your WebBrowser o navigate to http localhost 8181 to access inTB inTB login _ BGoOe Rog 3 Right ctrl 4 Figure 2 13 inTB ready to be used To do so minimize the black window open a browser Mozilla Firefox Internet Explorer Safari and on the address bar type http localhost 818 1 J D ine x MON S L localhost N TB Figure 2 14 Accessing inTB running locally If everything worked as expected you should now be using you
7. AE OS R k 20 322 Detailed results 222i ceda see deed uweg ar 21 3 3 is A III 22 Sod Symbols A ERE ORR ORS OER ORS ER ES Adding new Opti NS s cscs cmos ocea doe Brae ae Ware aya Selecting dates s eg e HG e EE e ee eee ee ee e 3 3 2 Single entry Using the forms lt 1030 rows Sees e ws Follow up information 40 ar eB RA eR eked G8 3 3 3 Multiple entries Pile upload a4 2 04 eed es aoe Bae He oS 4 Advanced Topics 4 1 Disabled Virtualization oe a oe ae aa ea RE RSE Se eee eS 4 2 Advanced access to database 4246046 e 4 bee be E EEE GEE 4 3 Increasing inTB resources lt lt ek ey ee eR eee ERR ER RES 44 Changing the system 2i22 4282644 4 82554 8o eh O40 dla 4 5 inTB in Production 5 Troubleshooting 6 Glossary Index CHAPTER ONE INTRODUCTION 1 1 What is inTB inTB is a data integration platform for molecular and clinical epidemiological analysis of My cobacterium tuberculosis inTB innovates not only by its extensive integrative nature and the ability to perform sophisti cated analysis but also by providing all this in a ready to use tool This contrasts with existing alternatives that typically require online access and upload of data to a server via the Internet With inTB there are no confidentiality or privacy concerns as your data never leaves your computer 1 2 What can I do with inTB You can use inTB to manage your clinical socio demographic and molecular data inTB has severa
8. Species strains along the years s SNP Percentage visualize SNP variation in collected samples Regions compare SNP variation grouping data by region where samples were collected Resistance correlate resistance to antibiotics with presence or absence of snp variants s Relapse Species visualize frequency of reinfection by different species Strains same as above for strains e Geographic Districts compare species variation by district Counties same as above for counties Citizenship proportion of cases by citizenship of affected patients e Age age distribution of infected patients s Treatment Previous treatment distribution of number of treatments per patient Interruption treatment duration before interruption e Gender gender distribution of patients Diseases proportion of diseases which are associated with tuberculosis infections e Resistance resistance variation over time s Reports generate PDF or CSV reports summarizing different variables 3 1 2 Browse Under the browse section you navigate existing data using the different pre defined filters Additionally you can perform a custom search with a multitude of personalized filters s Taxonomy navigate episodes filtered by species strain e Resistance navigate episodes filtered by antibiotics resistance e Geographic Districts episodes filtered by district 3 1 Navigation menu 18 inTB User Manua
9. care and not without comparing with each individual method 3 1 5 Download In this section you can download the present User Manual and also the VirtualBox images and the packages for advanced installation For more information on installation please refer to nstallation 3 1 Navigation menu 19 inTB User Manual Release 1 0 3 2 Data access 3 2 1 Summary results The results page gives an overview of the most relevant information for each patient At the top of the page information about how many episodes match the chosen criteria both with and without molecular data as well as instructions on how to interpret the table are provided Molecular clinical and socio demographic data of M tuberculosis episodes o Episodes with molecular clinical and socio demographic data 121 Episodes with clinical and socio demographic data 11410 inl B by default only shows information for episodes when there is also molecular typing information associated with the clinical episode IF you wish to see the clinical information for the episodes that you chose click below in the all data button Figure 3 2 Episode statistics The third column contains the number of episodes each patient had while the color of the number corresponds to the number of samples for each episode Each episode can have more than one sample The same column is also a link to the patient file where the user can see all the information about the curre
10. e 32bits image Linux Open a terminal and run the command egrep vmx svm proc cpuinfo and if any output including vmx or svm is generated it means your computer has hardware virtualization However if after importing and starting the image in VirtualBox you get the error enabled but is not operational Your 64 bit guest will fail to detect a 64 bit CPU and will not be able to boot a VT x AMD V hardware acceleration has been Please ensure that you have enabled VT x AMD V properly in the BIOS of your host computer Continue Close VM Figure 2 7 Virtualization is not enabled Refer to Disabled Virtualization under Advanced Topics to enable it 2 2 VirtualBox Setup 7 inTB User Manual Release 1 0 2 2 3 Importing inTB First you should download the correct VirtualBox image Read the section Picking the right format if you don t know which to choose Figure 2 8 How to import the inTB VirtualBox image Once the download is complete start VirtualBox and on the File menu select Import Ap pliance Figure 2 9 The Import Wizard Click on Open appliance and select the VirtualBox image you just downloaded click Open followed by Next 2 2 VirtualBox Setup 8 inTB User Manual Release 1 0 Figure 2 10 inTB s VirtualBox image details The Name should be inTB_x86 or inTB_amd64 for the 32 and 64bits images respectively After a few seco
11. e patient identifier will always be a required field For each patient inserted into the database the system automatically creates an episode num ber If the patient reappears into the system a new episode will be associated for this patient meaning the patient had at least two distinct clinical episodes 3 3 Adding data 23 inTB User Manual Release 1 0 When adding infection information the patient D can be omitted and instead a sample iden tifier will be required Not providing the patient D will store molecular information without being associated to a patient In the case that the user is inserting data for an existing patient with multiple episodes in an other block of information the user must specify the episode corresponding to the new data Since the episode is a number created by the system a link is provided to the patient file where all the information about the episodes is presented This facilitates the linking of different blocks of information The same reasoning is applied when inserting molecular and or resis tance data Additionally one can edit existing data by using the provided UPDATE forms They are iden tical in all to the INSERT counterpart with the exception that they will be rendered pre filled with existing information Follow up information During a follow up new samples may be collected and patient details may have changed since last visit To simplify the process when adding a follow up
12. e pressed is one of Delete F2 F8 F9 depending on the computer model If you can t find any option on the BIOS related with virtualization please go back to Picking the right format and use the 32 bits version 4 2 Advanced access to database In addition to the inTB web interface you can access the database directly by navigating to http localhost 8 18 1 phpmyadmin and login with user root and password intb The database is called intb This will allow you to change content and structure in a way which is not possible via inTB s interface Keep in mind that modifying the database directly may affect inTB s output and depending on the extent of the modification even cause it to fail 4 3 Increasing inTB resources Two things may affect significantly the performance of inTB while running inside VirtualBox memory and processing power both of which can be increased as long as sufficient resources exist on your computer 25 inTB User Manual Release 1 0 Additionally if you loaded large sets of data it may be that the system is running out of space The current space limit is set to 20GB If this is your case we recommend that you follow the Server install instructions to install inTB on a dedicated computer server To increase either memory or processing power stop inTB by closing the black window On the VirtualBox Manager window right click on inTB and select Settin
13. ed 1 4 Is it possible to use inTB for infections other than tuberculosis inTB was originally designed to be used with tuberculosis however with minor adjustments it can be adapted for other organisms If you have interest in using inTB for other organisms don t hesitate to contact us at http bioinformatics igc gulbenkian pt 1 3 Is inTB for the non technically savvy 2 CHAPTER TWO INSTALLATION 2 1 Alternatives inTB is available in two formats A ready to use VirtualBox image for quick installation and the traditional zip tar package for server installation 2 1 1 Quick Install In order to use the VirtualBox image you must first install VirtualBox Instructions for this can be found under VirtualBox Setup The easiest way to use inTB is to use the VirtualBox images If however you prefer to install it on a server for production please refer to Server install 2 1 2 Server install inTB can only be installed on a Linux Unix machine If you want to install it on MacOSX or Windows you will need to use the Quick Install approach In order to follow these instructions you should already have some knowledge about Linux and the Linux shell If at any point you feel lost don t hesitate to contact us at http bioinformatics igc gulbenkian pt In order to install inTB on your servers you have two options 1 Transfer all the content of the VirtualBox image to a local disk This option replaces any thing you have
14. gs On the newly presented window select System Here you can increase the amount of memory Try to prevent going into the orange red area or your computer s performance will suffer If you wish to increase processing power while still on the System section click on the Processor tab and increase the number of processors assigned to it Note If you don t have Hardware virtualization support you won t be able to increase the amount of processors For best performance in inTB at least 2048MB of Memory and 2 Processors are recommended 4 4 Changing the system If you wish to customize the system beyond what the web interface allows you to do you can access the virtual machine directly by logging in on the VirtualBox window The credentials are presented on screen If the screen is completely black move the mouse cursor over the black screen left click it and press any key on the keyboard The VirtualBox is running Ubuntu Lucid 10 04 inTB is built with Django 1 4 and all of its files can be found on var django inTB 4 5 inTB in Production The provided VirtualBox images are meant for testing purposes and limited use When using them in production some additional steps need to be taken to ensure the system remains secure These are beyond the scope of this manual are are indicated here simply as bullet points 1 Change password for user root 2 Change password for user root on MySQL 3
15. inTB User Manual Release 1 0 Patricia Soares Renato Alves August 12 2013 CONTENTS 1 Introduction 1 1 1 WhatisinTB ss ems 232 ote ea Ee cad 1 1 2 Whatcan Ido with mip sr pos rs rod eR ened 1 1 3 IsimTB forthe non technically Savvy 2 1 4 Isit possible to use inTB for infections other than tuberculosis 2 2 Installation 3 A he ae ee ee ee ga oe 3 Dold Quek IGG ues enee a R Be e Sw Rs T Bowes 3 Zoe A 3 2 2 NARI SEP a o a Bowe e e Bok Ai cda 4 22 1 Anstalling VirtualBox 2 5 4 4 soed bs dk sipin o Bob a jai dansi Bone 4 22 2 Picking the prel A 5 WIDIOWS oa rra A A AR 5 MacOS 05 0 pea See pies Sek p R a OH ee ES 7 LINUX e 242 Se ee a eee eee ES a e a ia Se HS 7 2 2 3 IPOD UB os view Ye Pew SA ES oe Pee oe Pee ee 8 224 Using VIQUAIBOR lt lt 2262542242234 e 82 10 2 2 5 Accessing inl B occiso 11 2240 Stopping inTB 24254454654 5465 455445 648 4448 12 20 Server installation 20ce cea hee ee ee eee EL eee EER EERE 13 2 3 1 Reusing VirtualBox content 224 42 4 48 44S444 44 a4 13 252 Installing from source gt ae yan es ek eee a 15 3 Usage 17 3 1 Navigation menu Y iia R R RRR de Seb R bei eaand 17 Sol Analyze AE 18 alld BONES Tesista tds daria 18 la Data Mp TTT 19 314 Diversity se eresas ada eA A Se RE 19 Slo Download a 2 4225 rr A Ga a Gei ah 19 Do Data acess Os oeann e s OS a g a HESS AS e eie oi e aiee aai pA ES 20 3 22 1 Summary results lt sea oe ea
16. information the user is presented with a copy of data inserted previously for the same patient If no information change you can simply confirm all intermediate steps 3 3 3 Multiple entries File upload While inserting single entries may be the most frequent use case we provide an alternative for bulk insertion of data Bulk insert can be useful when migrating data from other systems Note Please note that it s not possible to edit existing data using this approach Similarly to Single entry Using the forms the user has different options for data upload The only exception is follow up information which should be included in each file and distinguished by specifying the appropriate value under the column Type visit After selecting the type of information to be inserted the user is presented with an upload form and links to two template files One file without errors provides a reference for how data should be formatted The other with errors allows previewing the validation mechanisms present in inTB 3 3 Adding data 24 CHAPTER FOUR ADVANCED TOPICS 4 1 Disabled Virtualization If you have a recent computer but VirtualBox says it doesn t have hardware acceleration check that virtualization is enabled on the BIOS of your computer Some computers have virtualiza tion disabled by default The BIOS can be accessed by pressing a key imediately after powering on your computer Usually the key that needs to b
17. l Release 1 0 Counties episodes filtered by county e SNP explore all SNPs currently in the system and associated information s Time episodes filtered by year of infection e Samples display the molecular information of all samples in the system s Gender episodes filtered by year of infection e Search perform a custom search with user selected filters e List manage compare the episodes that were hand picked for comparison 3 1 3 Data Input This section includes the two existing approaches to add data to inTB For detailed information on adding data to inTB please refer to the Adding data section of this manual s Insert Edit Insert and update data in the system using a sequential set of forms s Upload Insert data in the system by uploading a CSV 3 1 4 Diversity In this section you can visualize trees built for each individual genotyping method as well as one tree supertree which tries to incorporate all information from all others methods into a single tree Reference species strains are also marked in the tree which allows automatic classification of all samples in the system e Dendrogram SNP tree built using SNP information MIRU VNTR tree built using MIRU information RFLP tree built using RFLP information Spoligotype tree built using Spoligotype information Supertree tree built by merging all results from the other four methods this method should be analyzed with
18. l validation mechanisms while adding data that ensure consistency and prevent human errors Once some data is present in the system you can analyse it Current analysis include s Frequency of infection by a given Species strain over time e Reinfection and relapse with same or different Species strains e Age distribution of infected patients e Gender distribution of infected patients e Co occurrence of diseases and behavior of infected patients Geographic distribution of Species strains Frequency of treatment abandonment e Drug resistance over time Generate yearly reports of different aspects of tuberculosis progression Follow tuberculosis evolution and occurrence of new variants inTB User Manual Release 1 0 1 3 Is inTB for the non technically savvy inTB is designed with end users in mind Its target audience are primarily clinicians and medi cal staff interested in extracting more information from existing data All of the provided analysis tools were successfully tested with a group of users mostly unfa miliar with tuberculosis Most charts plots were considered intuitive and easy to interpret For detailed descriptions proceed to the Usage section of this manual Installation was simplified by providing ready to use packages and detailed installation instruc tions Once installed you have all the tools required for the job at the distance of a mouse click Refer to the quick installation instructions to get start
19. mmediately or in the future Microsoft strongly recommends that you stop this installation now and contact the software vendor for software that has passed Windows Logo testing Continue Anyway STOP Installation Figure 2 2 Installation warning can be safely disregarded 2 2 VirtualBox Setup 4 inTB User Manual Release 1 0 If during installation you are warned multiple times about incompatible software please con tinue the installation anyway This warning if frequent in some versions of Windows in par ticular Windows XP and can be safely ignored Once VirtualBox is installed reboot if necessary you can now proceed to the installation of inTB 2 2 2 Picking the right format If you don t want to be bothered use the 32bits image If on the other hand you would like to get the best out of your computer while running inTB you should use the 64bits image However depending on your computer you might need to confirm if it supports Hardware virtualization and if it s active Detailed instructions are available for Windows MacOS and Linux Windows On Windows you can use the LeoMoon CPU V application to detect hardware virtualization Simply download the application at http leomoon com shop application leomoon cpu v and execute the provided file After a few seconds you should be presented with one of the following three scenarios Intel R Core T M i7 CPU 920 2 67GHz v11 05 15 Hardware Virt
20. nds you will see a summary version of what you are about to import To continue simple click Import Importing Appliance Importing appliance Z inTB 64bits owa bd Importing virtual disk image inTB 64bits disk1 vmdk 2 2 0 X Figure 2 11 Importing in progress After a few seconds minutes you should see a menu entry with the name inTB_amd64 if you chose the 64bits image or inTB_x86 if you chose the 32bits image inTB is now installed and ready to be used 2 2 VirtualBox Setup 9 inTB User Manual Release 1 0 2 2 4 Using VirtualBox On the VirtualBox interface right click the inTB entry on the list and select Start sg Oracle VM VirtualBox Manager Co lS ls File Machine Help w gt Bada New Settings Start Discard OVS inTB_amd64 E General E Preview 3 Wa Powered Off Name inTB_amd64 Operating System Ubuntu 64 bit System Base Memory 1024 MB 3 Boot Order CD DVD ROM Hard inTB_a md 64 Dis Acceleration WT x AMD Y Nested Paging PAE NX Display Video Memory Remote Desktop Server Disabled Storage Controller IDE Controller IDE Primary Master CD DYD Empty Controller SATA Controller SATA Port 0 inTB_amd64 disk1 vmdk Normal 20 00 GB gt Audio Figure 2 12 Starting inTB Note If you picked the 64 bits version and at this point you got an error mentioning VT x or AMD V read the Disabled Virtualization section
21. ns running an operating system as if it was an application This technology is also called VT x on Intel processors and AMD V or SVM on AMD processors CSV A Comma Separated Values CSV file Contains information in a spreadsheet like format which can be easily processed by other tools This format can easily be generated 28 inTB User Manual Release 1 0 from most software that can handle spreadsheets Examples include OpenOffice and variants Microsoft Office and iWorks Numbers among several others Patient identifier A numerical entry which identifies the patient Typically this would be the National Health identification ID This number is never displayed in inTB Sample identifier A alpha numerical entry which identifies a sample collected from a patient This field has no required format Typically this would be a sample code generated by genotyping or sequencing platforms Follow up Typically a medical visit after the first evaluation of the clinical status of the patient A follow up appointment can be performed before or after treatment has started 29 C Clinical form 28 CSV 28 E Episode 28 F Follow up 29 H H37RV 28 Hardware virtualization 28 M MIRU VNTR 28 P Patient identifier 29 R RFLP 28 S Sample 28 Sample identifier 29 SNP 28 Spoligotype 28 U User Manual 28 V VirtualBox 28 VirtualBox image 28 Z zip tar package 28 INDEX
22. nt episode ey Select Episode Multiples i 53 MEJO 469 2 soho let w SC Figure 3 3 Number of infections per patient The remaining columns contain graphical summaries of the most important information and more details are available by hovering the cursor over each of these icons By default the results table will only show the episodes that have associated molecular data although a link is provided to show all the episodes 3 2 Data access 20 inTB User Manual Release 1 0 Select Episode Multiples 1 K 2 Strain M 108 1 OY X SNP U MIRU VNTR SNI Clinical form Pulmonary pe Date of diagnosis 2008 01 09 Patient status Interruption or a 247 1 Abandonment NI Radiology No cavitated lesion pe Antibiotics resistance Sensitive Case definition New case wa 1 dh 7 TSN SI Figure 3 4 Clinical data Hovered with mouse 3 2 2 Detailed results The patient file presents information about the current episode of disease other episodes data on follow up and contact and a report of fields with missing information Patient 23616 Episode 2406 Figure 3 5 Patient file To visualize the molecular information associated to each episode the user has to click on the genotyping method name and the table will expand showing the information SNP polymor phisms are colored for quick identification Patient 23616 Episode 2406 SNP 6TCGTCGAABBaGccH csccccocOccQcBOcccrcatacccrcBrccccctaQas
23. ntifies the disk and the number identifies the partition number From the list of all disks you should identify which one corresponds to your server Make sure of this or you may accidentally delete all content from the wrong disk If you only have 2 disks connected on your computer including USB disks and pen drives you should have sda and sdb To know which one corresponds to your computer and which one to the server run mount grep sd It should print something with a similar structure to this dev sdal on type ext3 rw errors remount ro In the case above sda is my computer s disk which in turn makes sdb the server disk I have connected to it If you already had a system installed on your server s disk you may try to identify it simply by comparing the number of partitions in each disk or additionally by running mkdir mnt testdisk sudo mount dev sdb1 mnt testdisk or sdb2 sdb3 depending on your partition scheme and then checking the content of mnt testdisk for something that identifies it as your server s disk Before continuing make sure you run cd sudo umount dev sdbl1 Finally now that you are absolutely sure that sdb or whatever is your case is the server s disk run dd if inTB raw img of dev sdb 9 If all commands were successful so far you should now have inTB installed on the disk as a 20GB partition All remaining disk space will be left for
24. r local installation of inTB You can now start adding data via the INSERT EDIT or the UPLOAD menu entries Once some data is loaded the Browse and Analyze sections will be functional 2 2 VirtualBox Setup 11 inTB User Manual Release 1 0 2 2 6 Stopping inTB While working with inTB you should leave the black window minimized Once you are done you can close it and select Send the shutdown signal gt Close Virtual Machine Y leal 64 You want to L EA O save the machine state Send the shutdown signal F Power off the machine Cancel Help Figure 2 15 Stopping inTB A few messages will be displayed and the black window should close after a few seconds Note The inTB VirtualBox images are built with conservative limits If you find that the system crashes or becomes too slow to be usable read the section ncreasing inTB resources under Advanced Topics 2 2 VirtualBox Setup 12 inTB User Manual Release 1 0 2 3 Server installation 2 3 1 Reusing VirtualBox content Requirements e 20GB or bigger disk where inTB will be installed e An extra disk or usb drive for storing the raw image 20GB during the conversion pro cess Steps 1 2 If you already have VirtualBox installed you can skip to step 3 Download the Oracle VM VirtualBox software from http www virtualbox org or install it via your package repository Run Virt
25. tB cacccccccQaQGRsHpaBsstcachc MIRU VNTR Without information Spoligotype Without information RFLP Without information Figure 3 6 Molecular information in the patient file 3 2 Data access 21 inTB User Manual Release 1 0 3 3 Adding data When inserting data either through the web form or uploading a CSV file the user has to select which type of data to insert clinical socio demographic molecular resistance follow up or contact data For every type of data a patient identifier will be requested but it is not mandatory for molecular and resistance data where only a sample code is required This enables the asynchronous uploading of data that can later be linked when further data becomes available 3 3 1 Symbols used Adding new options While adding information in particular when the database is mostly empty a lot of the fields 99 will not include any options other than the no information representation Insert patient Patient Hospital 3 Process Type visit First diagnosis Figure 3 7 Adding patient information In order to prevent inserting different variations of the same information options already on the system are displayed for selection If the desired option is not yet present among the available ones one can click on the green plus sign in order to add it A window will show up prompting the user for new information Insert new entry Name
26. ted at var django inTB inTBsite settings py and change database connection details accordingly 2 3 Server installation 15 inTB User Manual Release 1 0 8 Configure mod_wsgi in Apache following the instructions at https docs djangoproject com en 1 4 howto deployment wsgi modwsgi 9 Configure Apache to serve the contents of the media folder located at var django inTB media and adjust MEDIA_URL on settings py accordingly 10 If everything went well you should now have inTB running locally 11 Additionally you should do step 5 of the inTB in Production section 2 3 Server installation 16 CHAPTER THREE USAGE 3 1 Navigation menu ANALYZE TIME SP RELAPSE GEOGRAPHIC AGE TREATMENT GENDER DISEASES RESISTANCE REPORTS TAXONOMY RESISTANCE GEOGRAPHIC SNP TIME SAMPLES _ GENDER SEARCH LIST DATA INPUT DIVERSITY INSERT EDIT DENDROGRAM UPLOAD ENTITIES TEAM Figure 3 1 inTB s navigation menu The menu is organized in 4 sections Analyze Browse Data Input and Diversity Additionally 4 buttons exist at the bottom of the menu with institutional Entities and Team and Download information and the present User manual 17 inTB User Manual Release 1 0 3 1 1 Analyze Under this section you have all the analysis you can perform in inTB with exception of the phylogenetic analysis which live under the Diversity menu section s Time the number of infected cases for all
27. ualBox On the menu go to File gt Import Appliance browse to where you downloaded the virtualbox image and select the ova image Only Use the 32bits ova image if your server doesn t support 64bits systems If you use the 32 bits image everytime 64bits is mentioned from now on replace it by 32bits Once importing is finished open a Linux shell On the shell type VBoxManage list hdds grep inTB 64bits and you should see something like Location home user VirtualBox Machines inTB_amd64 inTB 64bits disk1 vmdk The home user part will be used in the next step Using the Location from the previous line type VBoxManage clonehd your disk location inTB 64bits diskl1 vmdk inTB raw img format RAW Once the command finishes there should be a file called inTB raw img in your current folder The aim of this step is to transfer the contents of the inTB raw img to the disks of your server Since there is too much variability to cover here on how you can access your server and how its disks are configured the following instructions assume that you can connect your server disks into your current computer If you have your server disk connected to your current computer run 2 3 Server installation 13 inTB User Manual Release 1 0 ls dev sdx This should give you something like dev sda dev sdal dev sdb dev sdbl The first letter after sd ide
28. ualization is supported and is ENABLED CPU Architecture OS Architecture 64 64 ay x Sanrio VT x Enabled vY Y 2011 LeoMoon Studios Figure 2 3 Virtualization is present you can use the 64bits image 2 2 VirtualBox Setup 5 inTB User Manual Release 1 0 C 2 U Intel R Core T M i7 CPU 920 2 67GHz v11 05 15 Hardware Virtualization is supported but is DISABLED CPU Architecture E OS Architecture 64 pd Y X 2011 LeoMoon Studios Figure 2 4 Virtualization is disabled Refer to Disabled Virtualization under Advanced Topics to enable it C 2 U Intel R Core T i7 CPU 920 2 67GHz v11 05 15 64 64 VT x Supported y p VI x Enabled XK X 2011 LeoMoon Studios Figure 2 5 Virtualization is not available Your computer doesn t have hardware virtualization your only option is to use the 32bits image 2 2 VirtualBox Setup 6 inTB User Manual Release 1 0 MacOS Intel based MacOS systems have virtualization enabled by default You should be ok using the 64bits image However if after importing and starting the image in VirtualBox you get the error Failed to open a session for the virtual machine Win7 cia VT x is not available VERR_VMX_NO_VMX Figure 2 6 Virtualization is not enabled or not available Try the instructions on http support apple com kb TS2744 If the instructions don t work for you you 1l have to use th
29. you to partition to your needs 10 Additionally if you plan on using this setup as a public production system you should follow the steps below section inTB in Production 2 3 Server installation 14 inTB User Manual Release 1 0 2 3 2 Installing from source Requirements Steps 1 2 3 10MB for inTB 200 300MB for dependencies Some extra space for temporary files Download inTB Package from the Download section of inTB website Create the folder var django Unpack the contents of inTB Package to var django Install the following python dependencies either using your Linux package manager or manually using easy_install or pip django 1 4 0 MySQL python aka mysqldb 1 2 3 PIL aka python imaging 1 1 7 numpy 1 4 1 scipy 0 7 0 networkx 0 99 pygraphviz 0 99 chardet 2 0 1 reportlab 2 4 simplejson 2 0 9 biopython 1 54 pycairo 1 8 8 matplotlib 0 99 1 1 Install the following software Python 2 6 5 MySQL server 5 1 63 or above Apache 2 2 14 or above Apache s mod_wsgi 2 8 or above graphviz 2 20 2 clustalw 2 0 10 or above phylip 3 68 or above PhyML 3 0 or above Note Other versions of the software may work but were not tested Go into var django inTB data and load the provided SQL dump into a MySQL database you can delete the data folder afterwards Edit the config file loca
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