User Manual Dr. GPS Raghava and the MycoTB team May 13, 2010
Contents
1. Key O 20 D Add Remove q jiii gt 11 4 2 Insert Record Click on the Insert Record Menu This window will come You can insert the record in the table by two operation first is file and second 1s row by row If you are insert the record by file File should be in WordPad or excel format Select the table name for insert the record and click on the File button Browse the file by click on the Browse Button If you want replace the existing data from the table then check the Replace checkbox Your file has special character between table s fields that special character fill in the Field terminate by textbox If you want to insert the record for particular column then insert the column name and click on the Submit button Welcome Admin aaa Create Table Insert Record Browse Table Manage Record Manage Table Manage OrganismName Manage User Manage Database amp C Help Select Organism Name Select Table Insert Record From Mycobacterium tuberculosis Y aduplicatedgenes Location of Text File Po File in Excel or Wordpad format only Replace Table The contents of the file replaces the contents of the selected table for rows with identical O Replace Record primary or unique key Fields terminated by Lo The terminator of the fields Column names fyou wish to load only some of a table s columns specify a comma separated field list ral il gt 12 If you2. are insert the record by row by row Choose the table name from the Select Table drop down list and click on the Row button then fill the value of table s field If you want insert another row then click on the Add Row button and fill the value in another row and last click on the Insert Record button El Welcome Admin Create Table Insert Record Browse Table Manage Record Manage Table Manage OrganismName Manage User Manage Database C Help select Organism Name Select Table Insert Record From Mycobacterium tuberculosis y aduplicatedgenes v E orfid Cluster_Memberl Cluster_ Member Cluster_ Members Cluster_Member4 Cluster_Memberb Cluster_ A M A a ls i n EJ 13 4 3 Browse Table Click on the Browse Table Menu This window will come You can display the table s record Select the organism name then table will come in Select Table dropdown list then click on the Search button Table s record will come below in table format dEl Welcome Admin Create Table Insert Record Browse Table Manage Record Manage Table Manage OrganismName Manage User Manage Database amp Ci pa kh la orf orid protein_name length stat stop strand_direction function Ps NED O as a a O a Pam mow Ney pane Wim ws e e a tein O A paeit Pans mowa CC O A li tn tin PN Gk Pi OSD ok A eb
3. click on the Update button If you want delete the record check the Delete Column s check box and click on the Delete button Operator s Form Seles Insert Record Manage Record Admin Sign Out Mycobacterium uberculosis Y e x Po Search orfid protein_name length start stop strand direction function A recombination protein F hypothetical protein 1110000050 oB 2145812387287 DNA gyrase subunit 8 DNA gyrase subunit A 1110000070 NA B14 10828 hypothetical protein 1110000083 11874 12311 hypothetical protein 1110000090 ppi AD 12468 1306 iron regulated peptidyl prolyl cis trans isomerase 1110000103 Ni 426 13133 13558 hypothetical protein 1110000113 Nie 282 13714 13995 putative septation inhibitor protein hypothetical protein 1110000130 tpG A AA BB para aminobenzoate synthase component ll 11110000143 1881 15590 17470 Lo transmembrane serine threonine protein kinase B PKNB prot 1110000153 1296 17467 18762 Itransmembraneserinefhreonine proteinkinase A PKNA prote 1110000163 1476 18759 20234 IpenicillimbindingproteinPbpA 34100001771 we dA 3431n ANA acan ell dicoiaso nede tee Me Jh a a A 28519 E 24 5 3 Change Password Click on the Change Password Menu This window will come You can change your password EE Operator s Form Insert Record Manage Record Change Password Admin Sign Out Help Cha
4. the Display amp Delete Set Menu This window will come You can see the details of the SET and delete the SET You can delete the SET When you checked the Delete field and click on the Delete button then corresponding SET will be deleted ES User s Form Elx Simple Query Browse Table Complex Query Display Record By Set Display amp Delete Set Change Password Admin sign Out Help Query Number of eet Name ey Record D ser Table aduplicatedgenes Column arfidl RvOO01 SET 3 Table aduplicatedgenes Column Cluster_Member2 Rw0279c OR Table general Column length 1524 ON SET 5 Table oessentialgene Column Gene_symbol dna OR Table hmtbpersistance Column GENENAM 3 6 Change Password Click on the Change Password Menu This window will come You can change your password EN User s Form A Simple Query Browse Table Complex Query Display Record By Set Display 4 Delete Set Change Password Admin Sign Out Help Change Password Old Password New Password Conform Password p A Update 4 Admin Category When you click on the Login Menu This window will come and Administrator is fill his user name password and Category and click on the Login button Login simple Search Advance Search Administrator Operator Login Help Exit Mycobacterium Tuberculosis Datab
5. 03c Ay0642c Ayllb43c Ayllb44c Ay sade Ay04 Dc Ayllb45c R0463 0 47100 Browse Table orfid 1110021060 1110022730 1110023950 1110025143 1110031850 1110031870 1110033260 1110005033 1110006423 11710006433 1110006443 1110033923 1110004703 1110006453 1110004630 1170011009 select Organism Name Complex Query Display Record By Set Select Table Display amp Delete Set Mycobacterium tuberculosis Y Number of Record Display CS Cluster_ Member Ay2643 Ay2643 Ay2643 Ay2643 Ay2643 Ry2643 Ay2643 AyDb42c Avait Avait Avait Avait AyQo03c Avait A0503c 0 01 E Cluster_ Member AvO g6 Aw07396 Aw07396 Aw07396 Aw07396 Aw07396 Aw07396 Aubb430 A0643c A0642c A0642c A0642c Avlb42c Avlb42c Avlb42c 0 1410 aduplicatedgenes Cluster Members Ru2279 Ayv2106 Ayv2106 Ayv2106 Ayv2106 Fw2106 Av2106 Avite Ayllb44c Ayvllb44c Aylb43c Ayvlb43c Ayvlb43c Aylb43c Aylb43c 0 4700 Cluster_ Member4 Ay23o5 Fw 2305 Ayer Av2erd Ay2erd Ay2erd Ay2erd Aysadec Ayaad2c Ayaad2c Ay3332c Avdic Ayllbd4c Avllb44c Ayllbd4c 0 4701 Change Password Cluster_ Members Ry2614c Ry2614c Ry2614c Ay2305 Ay2305 Aw2305 Ay2305 Ay04 0c Ay04 Dc Ay04 Dc Ay04 Dc Ay04 Dc Ay3332c Ry3332c Ay3392c 0 4 ONE Admin Sign Out A 3 3 Complex Query Click on Complex Query Menu This window will come You can merge two or more than two
6. INSTITUTE OF MICROBIAL TECHNOLOGY BIOINFORMATICS CENTRE Dr G P S RAGHAVA LAB www imtech res in raghava Mycobacterium Tuberculosis Database Management Software MycoTB User Manual pE d d o 7 A Dr G P S Raghava and the MycoTB team May 13 2010 Contents l 2 3 Nn Welcome Pasaia die LOS Pa cio Foy ol ee A Pe Te OPT O Te er Sell ig dA PIO RUC ds eZ BOW e TaD IE axe seid S 3 COMPlEx OQU ea A a Display Record BY edilicias 29 ADISDIAY amp Delete Seti dd 320 Change Pass Woo AMINO Ale 8 OLY td ice dcir abad cee All Create Tale alas AnD iser INC COR ota Ae Browse Tale atadas 4A Manase AA A A A Manacor cocida 4 0 Manage Organism Name usada Ae Manase US cis 4 8 Manage Database amp ConnectiON ccccccccooooccnnnnncnnnonononnnnnnnnnnnnnnnos Operator Galeras A WAIST RC Oa eect eac hs eae eter ones senee D2 Manage RECOM erasian a a a ae 59 Chanse PassWord aia oi cc suesiatahertnncmueenieasnanin on 11 1 Welcome Page MycoTB Database software has successfully installed in your computer Then MycoTB Shortcut in your computer s Desktop Double click on the MycoTB Shortcut and welcome Page will come simple Search Advance Search Administrator Operator Login Help Exit Mycobacterium Tuberculosis Database Software About MTB Database Team Members Mr Garnav Mittal Problem Functional annotation Project Assistant of a proteome is one of the major challenges in
7. SET into single new SET When you want merge two SET then firstly select the organism name All SET will come in the Select Set dropdown list according to organism name If you find the record according to two SET then click on the Search button otherwise merge more SET then click on Add button and so on New SET is combination of two SET or more than two SET dEl User s Form Simple Query Browse Table Complex Query Display Record By Set Display Delete Set Change Password Admin Sign Out Select Organism Name Mycobacterium tuberculosis v AND Operator have higher priority to OR operator Select Set SET 1 Help OR v Add Remove Search of m q a Query Number of yi Name a Record JS Table aduplicatedgenes Column ortidl 40001 SET 3 Table aduplicatedgenes Column Cluster Member lt Rv0274c OR Table general Column length 15 4 SET 5 Table cessentialgene Column Gene_ gt oymbol dna OR Table hmtbpersistance Column GENENAME pon ES 3 4 Display Record By Set Click on the Display Record By Set Menu This window will come When you generate the SET then result come in the form of the orf for Example Rv0001 you can display record from one or more than one table according to the SET Firstly select the SET then all table come in the Whole Table list box When you select one or more than one table
8. and conform password and last click on the Reset Password If you want delete the existing user then select the user name and click on the Delete button If you want the change the category of user then select the user name from the Change Category box and select the another category and last click on the Update button Welcome Admin ada Create Table Insert Record Browse Table Manage Record Manage Table Manage OrganismName Manage User Manage Database amp C Help Create User Reset Password and Delete User Change Category ti gt 19 4 8 Manage Database amp Connection When click on the Manage Database amp Connection Menu You can take the backup of mtb database from the web server and restore database in the local wamp server You can update the connection information You can switch the connection to web server or local wamp server if you have server name or ip address user name and password If you want stable connection to the web server then fill the some information such as Server Name IP 172 141 121 22 User Name mtb Password Mtbimt22 If you want stable the connection to local wamp server then fill the some information such as Server Name IP localhost User Name root Password And last click on the Connection Update button If you want take the mtb database backup from the web server then firstly your connection is stables from the web server
9. and last click on the Update button If you want delete the table s field then check the Select column check box and click on the Delete Field button If you want delete the table from the organism name then select the table and click on the Delete Table HE Welcome Admin Create Table Insert Record Browse Table Manage Record Manage Table Manage OrganismName Manage User Manage Database 4 C Mycobacterium tuberculosis Y aduplicatedgenes v Add Field Delete Field Delete Table L T 3 Je k k Select Field Type Null Key Defaut Extra 0 o oom O a e O o ee ee E iemetas arses S o E wenes ares S o E oaet ares O o E one Menta arses eh O o E oertaal o o nh O emen as O o E maneto ares S o es E otr ent vaz ES o E omaes vot ES O o Ir E TE E EE a E al i gt 16 If you want add new field in the table then click on the Add Field button and display this window Enter the new field value choose the data type and set the position then click on the Save button Welcome Admin Create Table Insert Record Browse Table Manage Record Manage Table Manage OrganismName Manage User Manage Database amp C Help select Organism Name Select Table Mycobacterium tuberculosis y Add Field Delete Field Delete Table Length lf DataType is varchar Primary Key After Position boo sa protein_nam
10. ase Software About MTB Database Team Members LLLLLLL d MM DAS Le A Me ee oe LLL L e describes a function of MTb ORFs This system provides flexible system for annotating proteome and fer searching Category potential drug targets In order to make SysBorg more useful A R language based system called gt ysBorgTb htte sysborgth osdd netmras User Name Password LIE IAT eA OL OPYELOpe Was computer program comes from felemble system SysBorg designed under OSDD We are thankful to OSDD and CMMOT members for ther ideas im designing flexible systern Following are major contributors Mr Garuav Mittal G P 58 Raghava OSDD CRDD CSIR IMTECH By Default Administrator Name admin Password a4321 Category Admin Important Admin can change his password when you will do login 10 4 1 Create Table Click on the Create Table Menu This window will come You can create the new table in organism name Enter table name and give the number of table s field click on Go button then give the value of field s name and data type and click on the Save button then table will create Welcome Admin Create Table Insert Record Browse Table Manage Record Manage Table Manage OrganismName Manage User Manage Database 4 C Help select Organism Name Enter Table Name Number of Field Mycobacterium tuberculosis Y anndnabinderid o Field Data Type Length lf DataType is varchar Primary
11. e Add Remove Data Type SC start 4 Mm gt 17 4 6 Manage Organism Name Click on the Manage Organism Name Menu This window will come You can insert new organism name and edit the existing organism name If you want insert new organism name in the database then enter the new organism name in the New Organism Name text box and click on the Save button New organism name is come in the below table list You can edit the organism name when you select the organism name and type new organism name and click on the Update button You can delete the existing organism name When check the Delete column check box and click on the Delete button ES Welcome Admin Create Table Insert Record Browse Table Manage Record Manage Table Manage Database 4 Ci Help New Organism Name e FA Delete Organism Name ES d Mycobacterium tuberculosis ca io 18 4 7 Manage User Click on the Manage User Menu This window will come You can create new user delete existing user reset the password of existing user and change the category of the existing user If you want create the new user then enter the new user name in the Creat User Box and enter the password and select the category for the user and last click on the Save If you want reset the password of existing user then select the user name from the Reset Password box and enter the new password
12. erator By Default User Name mycotb Password m4321 Category User Important You can change their password when you will do login 3 User Category 3 1 Simple Query When User has login and Click on the Simple Query Menu This window will come You can filter the record from one or more than one table in single Organism Name Firstly you will select the organism name then all tables will come in Select Table dropdown list according to the organism name When you select table then table s field will coming in Select Field dropdown list If table s field type is character then equal to Y and not equal to operator will come in the Select Operator dropdown list otherwise equal to not equal to less than lt less than equal to lt greater than gt and greater than equal to gt operator will come in the Select Operator dropdown list When you select table field then first value of this field will come in the Value textbox You change the value of Value textbox to their according If you find the record according to this query then click on search button otherwise you want merge new query to this query then click on the Add button and repeat above process and so on If you click on the Search button means your query 1s complete We gives name to that query is SET 1 Query name cannot be repeat and change AND o
13. i tati f it uberculosis annotation ol ifs e E thankful to OSDD and CMIMOT proteome is still incomplete One members for ther ideas in of the problem in annotation of Category Operator designing flexible system proteome is managing data Following are major contributors generated during annotation There is a gap between existing Login Mr Gaurav Mittal data base management system Project Assistant DBMS and requirement of an Institute of Microbial Technology d TT T A G P 5 Raghava OSDD CRDD CSIR IMTECH By Default Operator Name entry Password e4321 Category Operator Important Admin can change his password when you will do login 21 5 1 Insert Record Click on the Insert Record Menu This window will come You can insert the record in the table by two operation first is file and second is row by row If you are insert the record by file File should be in WordPad or excel format Select the table name for insert the record and click on the File button Browse the file by click on the Browse Button If you want replace the existing data from the table then check the Replace checkbox Your file has special character between table s fields that special character fill in the Field terminate by textbox If you want to insert the record for particular column then insert the column name and click on the Submit button Eel Operator s Form See Insert Record Manage Record Admin Sign Ou
14. is user name password and category operator e Login Login menu is use for security purpose only Register admin user and operator can use this database f Help If you have not user name and password you are contact to Administrator and take his user name and password g Exit if you want to exit this software then click on the Exit menu 2 Login Page When you click on the Login Menu This window will come and user is fill his user name password amp category and click on the Login button El Login Advance Search Administrator Operator Login Help Exit Mycobacterium Tuberculosis Database Software Simple Search About MTE Database LL AE E po LUE ALVIE ool YLITLE one can addideletefmocdity any table or field using user tnendly interfaces Team Members User Name roto Dr GPS Raghava Scientist amp Head Biomftormatics Centre IMTTECH Institute of Microbial Technology Password Category SysBorg In 2005 first time attempt was made to design a flexible system for managing MTb data in order to improve the process of searching M Th G P 5 Raghava OSDD CRDD CSIR Chandigarh India Contribution This program is written under guidance of Dr Raghava He design concept and flowchart of this program IMTECH Default login names By Default Administrator Name admin Password a4321 Category Admin By Default Operator Name entry Password e4321 Category Op
15. iti tn tin PA plenk dl nu a Ss ell gt 14 4 4 Manage Record Click on the Manage Record Menu This window will come You can update and delete the record in the table Firstly search the record for delete or update by click on the Search button then record come in the table s row format If you want update the record then enter the modify value in the table s row and click on the Update button If you want delete the record check the Delete Column s check box and click on the Delete button El Welcome Admin Create Table Insert Record Browse Table Manage Record Manage Table Manage OrganismName Manage User Manage Database amp C Help select Organism Name select Table select Field Operator Enter Yalue Mycobacterium tuberculosis v length v 1524 Edit Record Delete orfid protein name length start stop strand direction function A Rtn MIC NA Ne O a a ct OO al tt MA Dr A TT A An i gt 15 4 5 Manage Table Click on the Manage Table Menu This window will come You can edit the table s field insert new field and delete the table from the organism name Select the table then table s field come in the below If you want modify the table s field name or change the Type then check the corresponding table s field by Select column check box and click on the Edit button Change the table s field or data type
16. nge Password Old Password Holelalatae New Password IA Conform Password II 25
17. perator have higher priority to OR operator means if single SET have more than one AND amp OR operator then AND operator between two query execute first to OR operator between two query ES User s Form ae Ed Simple Query Browse Table Complex Query Display Record By Set Display amp Delete Set Change Password Admin Sign Out A Select Organism Name Help Mycobacterium tuberculosis v AND Operator have higher priority to OR operator Select Table Select Field Select Operator Value EX Acconine to Table held aduplicatedgenes Y Cluster_Member2 k H Rv0279c AND k Add GENENAME Y no Lill Number of Query Record Table aduplicatedgenes Column orfid RvO001 349 Table aduplicatedgenes Column Cluster_Member2 Rw0279c OR Table general Column length 1524 6 3 2 Browse Table Click on Browse Table Menu This window will come You can display the table s record Select the organism name then table will come in Select Table dropdown list then click on the Search button Table s record will come below in table format You can increase and decrease width of table s cell when mouse over on the join of header cell according to screenshot orfid and Pattern1 then mouse s hand change to arrow then mouse drag left or right then width of cell will decrease and increase simple Query orf 12106 Av2279 Aw2305 Ry2614c Rv3185 Ayala DEEH Ay05
18. see above connection update then after click on the Database Backup button and dialog box will come for saving the database file location You give the backup file name and click on the save button Then your database will successfully backup If you want restore backup database in the local wamp server then click on the Restore Database button and dialog will come and double click on the database backup file If you want export the tables then check the table and click on the Table Export button After this dialog box will open for saving the file You can give the file name and click on the save button If you want import the tables then click on the Table Import button After this dialog box will open for taking the file s path You can select the file and click on the open button ES Welcome Admin Connection Manage Database root o ooo cee Connection Update al tialq O hmtbpersistance Table Import O general O sequence Table Export 20 5 Operator Category When you click on the Login Menu This window will come and Operator can fill his user name password and Category and click on the Login button Login simple Search Advance Search Administrator Operator Login Help Mycobacterium Tuberculosis Database Software About MTB Database Team Members LLL bl oo O bd LA AZ Despite world wide effort on UserName entry desiened under OSDD We are M Tubercules
19. t Help select Organism Name select Table Insert Record From Mycobacterium tuberculosis ho aduplicatedgenes v Location of Text File File in Excel or Wordpad format only The contents of the file replaces the contents of the selected table for rows with identical Replace Table Record Ll Replace primary or unique key Fields terminated by The terminator of the fields Column names f you wish to load only some of a table s columns specify a comma separated field list 22 If you are insert the record by row by row Choose the table name from the Select Table drop down list and click on the Row button then fill the value of table s field If you want insert another row then click on the Add Row button and fill the value in another row and last click on the Insert Record button Operator s Form Insert Record Manage Record Admin Sign Out Help Select Organism Name Select Table Insert Record From Mycobacterium tuberculosis k aduplicatedgenes orfid Cluster Memberl Cluster Member Cluster Member3 Cluster Member4 Cluster Member5 Cluster_ 23 5 2 Manage Record Click on the Manage Record Menu This window will come You can update and delete the record in the table Firstly search the record for delete or update by click on the Search button then record come in the table s row format If you want update the record then enter the modify value in the table s row and
20. the postgenormec era Despite world wide effort on M Tuberculosis annotation of its proteome is still incomplete One of the problem in annotation of Institute of Microbial Technology Chandigarh India Contibution He is main person behind the ceding of MycoTB All the program written by him including MySql interface and id 13 managing ci installation routines 1 G P 8 Raghava OSDD CRDD CSIR IMTECH a Simple Search Simple Search is use for Demo of Advance Search when you does not have the user name and password for this project Simple search is simiarly to the advance search but user can not store his query permanently for the future use when user generate query then we give the name to that query is call SET b Advance Search When you have user name and password then use the Advance Search user can store their SET for future use and generate further single SET between two or more than two SET Click on the Login menu and fill the user name password select category and do login c Administrator Administrator have the full control on the database Admin can Manage table Manage table s record Manage user and backup amp restore database etc But Admin do Login first with his user name password and category admin d Operator Operator have the limitation control on the database He can only insert and update the record in table But opearator do Login first with h
21. then table s field come in the Table s Field list box You can choose the table s field that you want to display and click on the Display button Table s field come in the below ES User s Form Ex Simple Query Browse Table Complex Query Display Record By Set Display amp Delete Set Change Password Admin Sign Out Help Select Set SET 1 a Whole Table Table s Field All aduplicatedgenes general orfid general protein_name hmtbpersistance general length oessentialgene general start sequence general stop general strand_direction general function protein name start stop Strand direction function AvOQ64 HA 68621 71559 hypothetical protein A DOB8 A 25301 76212 short chain dehydrogenase Avic gi 776139 Poe serine hydrosymethyltansterase Apr HA 20624 01673 glutamine transport transmembrane protein ABC transporter A0073 H A 01676 02669 glutamne transport ATP binding protein ABC transporter AVOOS2 chp 100583 102868 cation transporter P type ATPase A AvOlS4e MA 103710 104663 hypothetical protein Av0103c ctpb 119915 122173 cation transporter P type ATPase B R0109 PE_PGAS1 131382 132872 PE PGAS family protein Ry0124 PE_PGRS2 149533 150996 PE PGRS family protein AvO129e fbpC 156578 157600 secreted antigen 35 0 FBFC 85C antigen 85 complex C 46580 Mycolyl t Av0146 A 172211 173143 hyoothetical protein 3 5 Display amp Delete Set Click on
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