Life Sciences Towers. ApiDB Workshop Introduction. Logistics. Instructors. Jessica Kissinger June 26, 2006

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1 Life Sciences Towers C128 ApiDB Workshop Introduction Jessica Kissinger June 26, 2006 Parking Lot C Tower B Tower B116 Restroom A Tower Logistics Please, always wear your name tag There are no stupid questions Please do all exercises, they are cumulative Please attend all sessions, they are fairly organism independent Arrange for assistance in the evenings to get help with your particular research needs Read Getting the most out of bioinformatics resources before class tomorrow Building locked in evening ~7PM. Use C tower door Instructors See Course book for names and contact information ApiDB Co-PI s All Database Managers Expert users Database programmers Data Visualization students Center for Tropical and Emerging Global Diseases (CTEGD) at UGA 17 interdisciplinary faculty and their laboratories Cross-college and Institute (4), cross-department (7) Center, under the Office of the Vice President for Research (OVPR) To pursue cutting edge research on tropical and emerging global diseases, and train students in this field CTEGD s Goals Become a preeminent center for research and education in parasitic and other diseases in the world (our peers say we are getting close) Translate research results into medical and public health interventions for people at risk of these diseases (this is a long-range goal) Promote global and biomedical research and educational programs at the University of Georgia (we are working with others to accomplish this) Training is a large part of CTEGD s mission We all teach and train undergraduates, graduate students and postdocs CTEGD has been awarded 4 Training Grants to fund students (3 NIH, 1 Fdn) Faculty College/School Department Diseases Studied Don Champagne Agri.& Environ. Sci. Entomology Malaria; Chagas disease Mike Strand Agri. & Environ. Sci Entomology Parasitoid wasps; Innate immunity Dan Colley Arts and Sciences Microbiology Schistosomiasis (human & mouse) Jessie Kissinger Arts and Sciences Genetics Apicomplexa; Malaria; Crypto; Chagas Roberto Docampo Arts and Sciences Cellular Biology Malaria; Leishmanisis; Chagas disease Silvia Moreno Arts and Sciences Cellular Biology Toxoplasmosis; Leishmaniasis Kojo Mensa-Wilmot Arts and Sciences Cellular Biol. African trypanosomes; Leishmaniasis Boris Striepen Arts and Sciences Cellular Biol. Toxoplasmosis; Cryptosporidiosis Rick Tarleton Arts and Sciences Cellular Biol. Chagas disease (human & mouse) Harry Dickerson Veterinary Medicine Infectious Dis. Ichthyophthirius multifilis (Ich) of fish Julie Moore Veterinary Medicine Infectious Dis. Malaria (human & mouse) David Peterson Veterinary Medicine Infectious Dis. Malaria Pejman Rohani Institute of Ecology Ecology Infectious disease transmission Adjunct/Associate Faculty Ynes Ortega (Griffin) Agri & Environ. Sci. Food Sci. & Tech. Cyclosporiasis; Cryptosporidiosis Pat Lammie (CDC) Arts and Sciences Cellular Biol. Lymphatic filariasis Victor Tsang (CDC) Arts and Sciences Cellular Biol. Cysticercosis; Schistosomiasis Mark Brown Agri. & Environ. Sci. Entomology Malaria; Vector biology 1

2 Training is a large part of CTEGD s mission Introduction We all teach and train undergraduates, graduate students and post-doctoral fellows [so far,1 MCG MD/PhD candidate is training within the CTEGD] CTEGD has an NIAID/NIH T32 institutional training grant to support graduate students & post-docs here at UGA CTEGD has an Ellison Medical Foundation international exchange training grant to send and bring undergraduates, graduate students and post-docs to and from UGA CTEGD has 2 FIC/NIH D43 institutional training grants: 1 with Brazil (bioinformatics), 1 with Kenya (Kenyan graduate students & post-docs in Kenya and at UGA) Countries in which CTEGD faculty: Have ongoing programs Kenya, Argentina, Brazil, Peru, Haiti, Guyana Data integration and databases NIH Bioinformatic Resource Centers (BRC s) Databases and Queries Some History of the Apicompelxan databases Federation Our software Workshop specifics Have active contacts Ghana, Guatemala, Mali, Japan, Egypt Issues facing our community Bacterial Viral Parasitic Host Data preservation Data curation Data access Data integration Infectious Disease Paradigm Genomics Microarray Experimental systems Proteomic Genetics Immunology Host Pathogen Vector 2

3 Linking Biological and Computational Data to solve real problems The daily routine RAD EST DoTS clustering and assembly Identify coordinate regulation GUS Genomic alignment and comparative Sequence analysis Genes Proteins GO PATH Microarray Gene + Array Array + PATH Array BUILD YOUR QUERY, FIND A TESTABLE RESULT! Data The benefits of data integration Queries spanning data types become possible Systems approaches become become tractable for the average researcher Re-analyses become possible Patterns and trends become discoverable Commonalities in pathogen strategies? Host response? 3

4 BRC s brc/default.htm wards.htm NIAID Bioinformatics Resource Centers for Biodefense and Emerging or Re-Emerging Infectious Diseases Owen White:TIGR David Roos: UPenn Frank Collins: UND Rick Stevens: U of C Elliot Lefkowitz: UAB Richard Scheuermann, UTSMC Bruno Sobral:VBI John Greene:SRA Category A Bacillus anthracis, Clostridium botulinum, Francisella tularensis Variola major virus, Arenavirus, Hanta virus, Rift Valley fever virus, Ebola virus, Marburg virus, Dengue virus Yersinia pestis Category B Burkholderia mallei, B. pseudomallei, Clostridium perfringens Toxoplasma gondii, Cryptosporidium parvum Staphylococcus aureus, pathogenic vibrios, Listeria monocytogenes, Campylobacter jejuni California encephalitis group virus, Kyasanar forest disease virus, Omsk hemorrhagic fever virus, West Nile virus, Alphavirus Giardia lamblia, Entamoeba histolytica, Microsporidia, Ricinus communis Diarrhaegenic E. coli, Yersinia enterocolitica, Shigella, Salmonella Rickettsiae species, Brucella species, Coxiella burnetii, Calicivirus, Hepatitis A virus 4

5 Category C Plasmodium species Anopheles gambiae, Aedes Aegypti, An. Funestus, Culex pipiens, Ixodes scapularis Streptococcus pyogenes, Streptococcus pneumoniae Hantaan virus, Puumala virus, Crimean-Congo hemorrhagic fever virus, Yellow fever virus, Tick-borne encephalitis, Nipah virus, Equine morbillivirus Multi-drug resistant Mycobacterium tuberclosis, Influenza virus Rabies virus, Coronavirus ApiDB overview ApiDB (Apicomplexan Databases) is an NIH BRC It is an umbrella database that talks to the three component database, CryptoDB, PlasmoDB and ToxoDB ApiDB has tools and queries to support unified apicomplexan studies of sequence, orthologous genes and biochemical pathways What is a database? Lots of flat Data Files In its simplest form, it is a collection of data Computational databases can be flat file Relational Object oriented General searches vs a Query Relational Schema General searches of flat files, like find in Word or web page content searches at yahoo or Google look for the appearance of word within some text and in the case of web searches, return the entire page containing the found item Queries are structured searches of stored terms or features contained in a structured database, usually relational. What is returned, depends on what is asked. 5

6 What is a Tool? Tools operate outside of the relational framework. They usually function on flat files. Examples are BLAST, pubcrawler, custom motif tool, PlasmoAP, CYC pathway tools Sometimes the results from tools can be stored in a relations data base for later searches What are external resources? Resources outside the ApiDB family of databases Examples include, NCBI Genbank, KEGG metabolic database, OrthoMCL- DB, web site of data donors, WHO web site etc. A Little History PlasmoDB was born in June 2000 PlasmoDB ToxoDB CryptoDB ApiDB 6

7 ApiDB.org 7

8 Our Software Tools GUS schema WDK (Web Development Kit) The Databases:

9 We need your help How do you, the user, logical sort data and expect to find it in the databases? Intro and exit surveys Query sorting exercise Interactive studies of computer usage Interviews Suggestions and feed back Course Exercises Course computers - use the same computer for the entire workshop Login = apicomplex (click on name) Password = daydabaz23 Open a browser (Safari, Firefox) Printing - select print from your browser or application. The lab laser printer is preconfigured. We have supplied the printer with 3-hole punch paper so you can keep results in your binder if you choose to do so Course Web Site The web site (exercises and and answers) will remain posted to facilitate your transfer of information. It is not necessary to print everything. Funders Acknowledgements NIH - ApiDB Contract HHSN C Burroughs Wellcome Fund ApiDB Team ToxoDB and PlasmoDB Team at UPENN CryptoDB and ApiDB Team at UGA 9