Bioinformatics databases & software

A major focus of the field of bioinformatics is the use of computer software programs to facilitate biological research. This web site provides links to a variety of software tools that are freely available on the World Wide Web. Many other packages require the purchase of a license (even for academic use) from the company or organization that owns the software. Some licenses are university-wide (i.e. anyone can use the software).

Software developed at Johns Hopkins/Kennedy Krieger

Software/database Development
  • The Cardiac Gene Expression Knowledgebase (CaGE)
 Michael Bober, Rai Winslow
Christopher Bouton, J. Pevsner
Carlo Colantuoni, S. Zeger, J. Pevsner
Rafael Irizarry, Laurent Gautier
Ingo Ruczinski
Stuart Ray

Software available at the KKI Bioinformatics Center

  • Bioinformatics tools: GCG (JHU university-wide license: contact Jeremy Hankins, Biophysics, SOM)
  • Bioinformatics tools: Vector NTI
  • Bioinformatics tools: EMBOSS
  • Microarray data analysis: MatLab
  • Microarray data analysis: Scion Image
  • Microarray data analysis: J-Express (MolMine)
  • Microarray data analysis: GeneSight
  • Microarray data analysis: Partek
  • Microarray data analysis: Spotfire (JHU university-wide license)
  • Microarray packages: GEMTools (Incyte)
  • Microarray packages: MicroArray Suite (Affymetrix)(JHU university-wide license)
  • Microarray packages: Pathways (Research Genetics)
  • Microarray packages: AtlasImage (Clontech)
  • Phylogeny software: PAUP
  • Phylogeny software: Phylip
  • Phylogeny software: Mega
  • Statistics packages: S-PLUS (JHU university-wide license)
  • Statistics packages: Statistica
If you have any comments, suggestions or additions to this page please send them to: bioinf@kennedykrieger.org