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The AfCS Bioinformatics Laboratory

The AfCS Bioinformatics Laboratory. AfCS. 2002. The AfCS Data Coordination and Bioinformatics Laboratory. AfCS. 2002. Goal 1 Acquire, Process, and Disseminate Information. The AfCS Website (www.afcs.org). AfCS. 2002. WebMaster: Stephen Lyon Web related design: Stephen Lyon

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The AfCS Bioinformatics Laboratory

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  1. The AfCS Bioinformatics Laboratory AfCS 2002

  2. The AfCS Data Coordination and Bioinformatics Laboratory AfCS 2002 Goal 1 Acquire, Process, and Disseminate Information

  3. The AfCS Website (www.afcs.org) AfCS 2002 WebMaster: Stephen Lyon Web related design: Stephen Lyon Brad Kroeger Dawn Cotter Timo Hannay (NPG)

  4. The AfCS Website (www.afcs.org) AfCS 2002

  5. The AfCS Website AfCS 2002 Website Users Website Developers • Anonymous Public • Registered Public • AfCS Personnel • Content Contributors • Website Developers • Overall Development • Molecule Pages • Protein Lists • Experimental Data • Reports • Database Search Utilities

  6. AfCS Website Content AfCS 2002 Website Content • Public Areas • About AfCS • Data • Home • Login • Membership • Molecule Pages • Protein Lists • Protocols • Reports • Signaling Maps • Sponsors • Restricted Areas • Access Control Administration • Protein List Administration • E-mail Aliases • Progress Reports • View • Upload • System Committees • Message Boards • Barcode • Data • DataScope

  7. Overview of Access Control Layers HTTP request from user HTTP response from server Apache mod_perl Static HTML Perl CGI Java servlets Oracle database AfCS 2002 Access Control Layers 1. Web server layer:General access control for all users of the website 2. Application layer:More specific access control and personalization for users of each application (username can be read from cookie set by Layer 1) 3. Database layer:Database gives different access privileges to each application

  8. Page Types & Access Control AfCS 2002 User Request User Database WebServer Access Check Static Pages Program Access Check Dynamically Generated Static Pages Dynamic Pages

  9. AfCS Bulletin Board AfCS 2002 The primary purpose of the bulletin board is to facilitate the exchange of ideas, documents and data between Alliance members and provide the public a forum for providing feed back.

  10. AfCS Bulletin Board AfCS 2002 • Posting featuresdefine by the board administrator or moderator • Security featuresdefined by the board administrator or moderator • Formatting featuresuser controlled • User profile featuresdefined by the user board administrator • Searching features

  11. AfCS 2002

  12. AfCS 2002 Topic Views On line documentation Search and administration

  13. AfCS 2002

  14. The AfCS Data Coordination and Bioinformatics Laboratory AfCS 2002 Goal 2 Design and Develop a Laboratory Information Management System

  15. AfCS Barcode/LIM System AfCS 2002 Lothar Krause Madhusudan Lonnie Sorrels (SWMED) Ron Taussig (SWMED) Dallas Expt. Lab. Yuhong Ning Ilango Vadivelu Peter Morrison

  16. AfCS Barcode/LIM System AfCS 2002 Facilitate Sample Tracking Standardize Data Inputs/Outputs Automate Data Transfer between Labs Maintain Data Integrity

  17. AfCS Data Flow AfCS 2002

  18. Treatment GUI AfCS 2002 Inputs Cell Prep ID and yields unique treatment and sample IDs. This application also requires a protocol that is tied to the assay for which the sample is created, e.g. Western, Microarray etc. It captures the treatment details including incubation conditions, cell density, ligand and its concentration and time of exposure. This GUI also functions as a query tool. By entering an ID into the ‘Experiment ID’ and clicking on ‘barcode’, it re-loads the data previously submitted for that ID.

  19. Treatment GUI AfCS 2002

  20. Treatment Tables AfCS 2002

  21. Barcode GUI AfCS 2002

  22. Protocols: Interaction of the GUIs AfCS 2002 Reagent GUI Barcode Solution GUI Barcode Printed protocol with barcode Protocol GUI Ligand GUI Barcode

  23. Protocol GUI AfCS 2002

  24. Solution GUI AfCS 2002

  25. Reagent, Ligand & Solution Tables AfCS 2002

  26. The AfCS Data Coordination and Bioinformatics Laboratory AfCS AfCS 2002 2002 Goal 3 Create Efficient Internet Sites for Deposition, Inspection, and Utilization of Primary and Processed Data

  27. AfCS Data Store AfCS 2002 Robert Sinkovits Dennis Mock Brad Kroeger Chic Barna Richard Schuermann (Visitor) Yuhong Ning

  28. Data handling AfCS 2002 • Data transfer from Dallas/Caltech  SDSC • Parsing of transfer log files to identify new data • Parsing of data files / database loading • Generation of graphics, tables, etc. • Displaying results for ligand/assay • Data Curation • Update of ligand screen page • Ligand descriptions

  29. Parsing log files / loading db AfCS 2002 • Set of four cron jobs (microarray,cAMP, Ca++,Western blot)run each night. Names of newly uploaded files passed as arguments to loader scripts. • Log files created so that experiment schemas can be easily repopulated micro loader micro@afcs micro master cAMP loader cAMP@afcs cAMP master auto-ftp log Ca loader Ca@afcs Ca master western loader western@afcs western master

  30. Graphics generation AfCS 2002 • Scripts generate libraries of static images, html, tab-delimited files. Data pulled from experiment and barcode schemas • Ligand screen data directories purged and reloaded with new graphics, etc. barcode@afcs micro@afcs micro process data/micro cAMP@afcs cAMP process data/cAMP Ca@afcs Ca process data/Ca western@afcs western process data/western

  31. Display AfCS 2002 • Argument passed to CGI script to specify graphics, etc. to be displayed data/Ca Text, graphics, links, etc. for Ca assay 0.3 uM anit-Ig using B cells cal_ligscr.cgi AIG_0.3_uM_BC

  32. Ligand screen display (partial) AfCS 2002

  33. AfCS 2002 Ca++ display Automatically generated graph of Ca++ time courses for B cells treated with Antigen (Anti-Ig). Curves color coded by experiment.

  34. AfCS 2002 cAMP display Automatically generated bar graph of cAMP assays for B cells treated with Prostaglandin E2.

  35. AfCS 2002 Western blot display Automatically generated graph of phosphoprotein immunoblot results for B cells treated with CD40 Ligand.

  36. AfCS 2002 Western blot display Automatically generated graph of phosphoprotein immunoblot results for B cells treated with IL-4. Large pSTAT6 response plotted on right axis.

  37. AfCS 2002 cDNA display Clicking on cluster returns annotation for all clones belonging to cluster

  38. AfCS 2002 cDNA Analysis Interface • Array display and analysisfor AfCS Members

  39. Data flow overview: Ca++ AfCS 2002 SDSC server SWMED log data graphics SRB cal_master.pl cal schema cal_loader.pl barcode schema cal_graph.pl public.html curate.cgi internal.html display.html cal_disp.cgi

  40. The AfCS Data Coordination and Bioinformatics Laboratory AfCS 2002 Goal 4 Design and Implement the Infrastructure for Molecule Pages Database

  41. AfCS 2001

  42. The AfCS Molecule Pages AfCS 2002 Joshua Li Yuhong Ning Warren Hedley Brian Saunders TBK Reddy (BW) Andrea Maer (BW) Yousheng Chen Derren Barken (UCSD) Timo Hannay (NPG) Nicole Tindill (NPG) & Dallas AfCS Team

  43. MP Features AfCS AfCS 2001 2002 • A comprehensive literature-derived, object-relational database of signaling molecules • Distributed data entry by experts • Link to AfCS experimental data • A dynamic source of protein interactions with genomic and domain data from other databases • Definition of the “Functional State” of each signaling protein

  44. Molecule Pages – Author-Entered Data AfCS 2002 • The author is responsible for entering information about • AfCS protein’s functional states • Interactions of their protein with other proteins, and small molecules • Mutations of the protein, and their consequences and/or phenotypes • Relevant experimental information

  45. Molecule Pages – Automated Data AfCS 2002 • “Automated Data” for each protein is provided to both the public and the authors, and can be referenced by the author when entering their own data • The types of automated data made available will include: • Summaries of and links to external database records that correspond to, or are related to, the author’s protein • (e.g., Genbank, SwissProt and PDB records)

  46. System Architecture AfCS 2002 • The Molecule Pages website is generated by a 3-tier application • The web and middle tiers are Enterprise Java application running on the “Oracle Components 4 Java (OC4J)” application server • The database tier is Oracle 8.1.7

  47. Molecule Pages Multi-Tier Infrastructure AfCS AfCS 2001 2002

  48. Ontology AfCS 2002 Ontology: Ontology in the database world associates definition and knowledge about objects contained in the database. The knowledge pertains to properties of the object and its relationships to other objects coded as tables or indexes.  E.g., Ion channel: Object properties: sequence, structure, gating, kinetic…etc. Relationships: other channels, physiology, cell locations, diseases…etc.

  49. Database schema for antibody AfCS 2002

  50. PhysicalData Model for Molecule Pages AfCS AfCS 2001 2002

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