David Gilbert's Bioinformatics resources

Organisations / information centres / general resources

• European Bioinformatics Institute http://www.ebi.ac.uk
• International Society for Computational Biology www.iscb.org
• Human Genome Project Information
• Genome http://www.yourgenome.org
• National Center for Biotechnology Information http://www.ncbi.nlm.nih.gov
• The Bioinformatics Resource http://www.hgmp.mrc.ac.uk/CCP11/index.jsp

Funding / scholarships etc

• Fulbright scholarships

Journals

• Some journals etc
• See the general list at www.iscb.org/journals

Conferences

• See the general list at www.iscb.org

Jobs

• See the ISCB jobs list

Reading

• http://www.brc.dcs.gla.ac.uk/~drg/bioinformatics/reading.html

On-line reference / tutorial materials

• Biology:
  • http://industry.ebi.ac.uk/~brazma/Biointro/biology.htm (v good, for computer scientists).
  • http://www.ultranet.com/~jkimball/BiologyPages/ (detailed explanations on terms)
  • http://www.biology-online.org/ (comprehensive)
  • http://gened.emc.maricopa.edu/bio/bio181/BIOBK/BioBookTOC.html (on-line biology book)
  • http://www.nhgri.nih.gov/DIR/VIP /Glossary/ (glossary of genetic terms)

• Bioinformatics:
  • http://www.bioinformatik.de/
  • Genome Glossary

Legal / Intellectual property

• US law: genetics & patenting

Applications

• Alphabetical list from HGMP

Databases and tools

• Assorted databases via EBI
• Assorted tools via EBI.

  Sequence

  • Swiss-Prot Database http://www.expasy.ch/sprot/sprot-top.html
  • Pattern discovery in biosequences: http://industry.ebi.ac.uk/~brazma/patterns.html
  • Similarity searches in sequence databases http://expasy.cbr.nrc.ca/tools/#similarity
  • Pattern & profile searches in sequence databases http://expasy.cbr.nrc.ca/tools/#pattern
  • Sequence alignment tools http://expasy.cbr.nrc.ca/tools/#align

  Protein structure

  Protein structure databases

  • EBI Macromolecular Structure Database http://msd.ebi.ac.uk
  • Protein Data Bank http://www.rcsb.org/pdb
  • PDB Lite http://www.pdblite.org/
  • CATH Database of Folds http://www.biochem.ucl.ac.uk/bsm/cath
  • SCOP Database http://scop.mrc-lmb.cam.ac.uk/scop
  • Structural Genomics http://www.structuralgenomics.org

  Structure comparison

  • 3D Search http://gene.stanford.edu/3dsearch
  • DALI http://www2.ebi.ac.uk/dali
  • TOPS protein topology web page http://tops.ebi.ac.uk/tops
  • TOP pairwise/multiple alignment and similarity search http://bioinfo1.mbfys.lu.se/TOP
  • VAST structure comparison http://www.ncbi.nlm.nih.gov/Structure/VAST/vast.shtml

  Structure prediction

  • JPRED secondary structure prediction server (Geoff Barton)
  • PSIpred server: secnadry structure prediction, transmembrane topology, fold recognition (David Jones).

  Biochemical networks

  • PFBP http://www.ebi.ac.uk/research/pfmp
  • KEGG http://www.genome.ad.jp/kegg/
  • BRENDA http://srs6.ebi.ac.uk/ http://www.uni-koeln.de/math-nat-fak/biochemie/ds/dsbren_e.htm http://www.brenda.uni-koeln.de
  • PathDB http://www.ncgr.org/research/pathdb/
  • SRS http://srs6.ebi.ac.uk/
  • MPW-EMP http://srs6.ebi.ac.uk/ http://wit.mcs.anl.gov/WIT2/
  • CSNbd http://geo.nihs.go.jp/csndb/
  • Transfac http://transfac.gbf.de/
  • RegulonDB http://www.cifn.unam.mx/Computational_Biology/regulondb/
  • DPinteract http://arep.med.harvard.edu/dpinteract/

Courses

• Bioinformatics course: http://cmgm.stanford.edu/biochem201
• Introduction to Bioinformatics for computer science undergraduates: www.brc.dcs.gla.ac.uk/~drg/courses/bioinformatics
• Max Plank Institute for Molecular Genetics
• Mark Craven's Home Page
• Attwood: BIOINFORMATICS PRACTICAL
• The Brutlag Bioinformatics Group - Courses