Resources for Research in Medical Computing

Contents

• Chemical, Biological, and Medical Databases
• Literature
• Chemistry
• Protein Structure
• Genetics
  
• Tools
  
• Interesting Projects and Organizations in Medical Computing Research
• Information Hubs
  
• News, Blogs, and Feeds
  

Chemical, Biological, and Medical Databases

Literature

PubMed is a database for literature medical and biology developed by the National Center for Biotechnology Information (NCBI) at the National Library of Medicine (NLM).  It contains abstracts from more than 4,800 biomedical journals.

Chemistry

National Library of Medicine, PubChem web site at pubchem.ncbi.nlm.nih.gov provides information on the biological properties of small molecules. You can use the structure search facility to find properties and structure of many chemicals.  It is a component of the US National Institute of Health's (NIH) Molecular Libraries Roadmap Initiative.

Argonne National Laboraties host the WIT (What is There?) database containing comparative analysis of sequenced genomes.  Argonne National Laboraties also hosts EMP (Enzymes and Metabolic Pathways) and other databases.

Protein Structure and Sequence

The US National Center for Biotechnology Information (NCBI) Entrez Protein Database is compiled from a variety of sources, including SwissProt, PIR, PRF, Protein Data Bank (PDB). A copy of the Protein Data Bank (PDB) hosted by the Research Collaboratory for Structural Bioinformatics (RCSB) can be found at at www.rcsb.org/pdb.  The latest additions to the PDB can also be browsed and downloaded at www.rcsb.org/pdb/smartSubquery.do?smartSearchSubtype=LastLoadQuery.  The Basic Local Alignment Search Tool (BLAST)  is a program that compares nucleotide or protein sequences to sequences in these and other similar databases.

The Swiss Institute of Bioinformatics (SIB) hosts the ExPASy (Expert Protein Analysis System) proteomics server, which includes a protein knowledge base and tools.

The Sanger Institute maintains the Protein Family (Pfam) database at www.sanger.ac.uk/Software/Pfam.  Seventy four percent of protein sequences have at least one match to at least one entry in Pfam.

Genetics

Completed in 2003, The Human Genome Project took many advances in computing to complete.  Among the goals of the project directly relating to computing are storing the DNA sequence information in databases openly accessible from the Internet and improving tools for data analysis.  The human genome can be browsed with the Human Chromosome Launchpad.  The GenBank database hosted by the NCBI is a DNA sequence database with genetic data from humans and other organisms.  GenBank can be most easily browsed with MapViewer. ENTREZ is the NCBI's search engine, which searches in GenBank and other NCBI databases.  The NCBI has a number of tools available for analysis, including BLAST.  The European Bioinformatics Institute has similar genetic databases and tools for working with the data.

The Institute for Genomic Research (TIGR) also hosts a genome sequence database also hosts serveral genome databases, including the Expressed Gene Anatomy Database (EGAD) at www.tigr.org/tdb/egad/egad.shtml.

The Kyoto Genes and Genome (KEGG) database is another genetic information database but also has pathway, ligand, and drug information and has a web services API to access the database.  Genome.net is a bioinformatics gateway hosted by the Bioinformatics Center at the Institute of Chemical Research, Kyoto University.  It includes KEGG and other bioinformatics databases.

Weissmann Institute of Science, GeneCards Database at www.genecards.org is integrated database of human genes that includes genomic, proteomic, and transcriptomic information.

Tools

EMBOSS is an open source tool for working with data from GenBank.

GrailEXP is an Experimental Gene Discovery Suite that can be used to predict gene locations in genome data developed by the Genome Analysis and System Modeling Group of the Life Sciences Division of Oak Ridge National Laboratory. The Oak Ridge National Laboratory has also developed PROSPECT (PROtein Structure Prediction and Evaluation Computer Toolkit), a protein structure prediction system.

GENSCAN is a gene finding program developed by Chris Burge and Samuel Karlin.  A web interface to the program is available at genes.mit.edu/GENSCAN.html.

PROCRUSTES is a gene recognition program that uses spliced alignment to explores possible all exon assemblies within DNA sequences.

GeneWise is a program that searches for genes by comparing a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors.  A web interface for the program is hosted by the European Bioinformatics Institute at www.ebi.ac.uk/Wise2/.

Biojava is an open source project initiated by Great Britain's Sanger Institute and hosted by the Open Bioinformatics Foundation. It focusses on genetic analysis.  The introductory article BioJava -- Java Technology Powers Toolkit for Deciphering Genomic Codes describes the project. 

Interesting Projects and Organizations in Medical Computing Research

There are computer systems to aid in medical research and there is also research in medical computer systems themselves.  Since the goal of both is the same, to move progress our ability to help people live longer and healthier lives, I will discuss both.  There are so many different things that researchers are trying to acheive and these are two of the hottest areas in science and technology at present.  There is some exciting stuff in this area but the best I can hope to do is to get a sample of what is out there and get peoples opinions on the it and on barriers that researchers face.

World Community Grid

Here (www.worldcommunitygrid.org)  is a software system with a lofty goal.  I have it installed on all three of my systems (two at work and one at home) and run it night and day.  It uses a grid of computers to solve various problems that are very computationally expensive.  The problem that it is working on now is FIGHTAIDS@HOME.  It analyses how potential drug molecules fit into the HIV protease and notes that the best candidate will be lab tested.   The software executing in the grid at present was written by The Molecular Graphics Laboratory at the Scripps Institute.  The grid software was made and is operated by IBM along with a very worthy collection of partners listed on the site.  The World Community Grid has also run the computations for The Human Proteome Folding Project.