Software at UCSF

Definition
A general term primarily used for digitally stored data such as computer programs and other kinds of information read and written by computers.
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Academic Research Systems

Contact: Rick Larsen (415) 502-4854 Rick.Larsen@ucsf.edu

  • MyResearch
Mission Bay

Cancer Center Computational Biology Core

Helen Diller Family Comprehensive Cancer Center, Mission Bay
Contact: Adam Olshen 415-514-9406 olshena@biostat.ucsf.edu

  • R (Bioconductor and custom packages), Gene Pattern, GSEA
  • Software development and tools
Mission Bay

Center for Advanced Technology

Biochemistry and Biophysics, Mission Bay
Contact: General Inquiries 415-418-3658 eric.chow@ucsf.edu

  • GenePix Pro 6.0
Mission Bay

CFAR Population and Clinical Sciences Core

Center for AIDS Research, Mission Bay
Contact: Jeffrey Martin 415-514-8010 martin@psg.ucsf.edu

  • Statistical and database management software
Mission Bay

Gladstone Bioinformatics Core

Gladstone Institutes, Mission Bay
Contact: General Inquiries bioinformatics@gladstone.ucsf.edu

  • Simulation programming with R / Perl / Python
Mission Bay

Gladstone Neurobehavioral Core

Gladstone Institute of Neurological Disease, Mission Bay
Contact: General Inquiries Michael.Gill@gladstone.ucsf.edu

  • HomeCageScan and SocialScan Videoanalysis software (CleverSys)
  • Noldus EthoVision Videotracking software
Mission Bay

Sequence Analysis and Consulting Service

Resource for Biocomputing, Visualization, and Informatics, Mission Bay
Contact: Scooter Morris 415-514-4406 scooter@cgl.ucsf.edu

  • Alignments -- pairwise and multiple alignment tools for sequences
  • Cytoscape network analysis
  • EMBOSS Software
  • Genome tools -- gene finding, comparing gene locations across species
  • Phylogenetics tools
  • Transmembrane segment prediction and display programs -- HMMTOP, Memsat, TMHMM, and TOPO2
  • W2H interfaces to EMBOSS
Parnassus

Biological Imaging Development Center

Departments of Pathology and Laboratory Medicinie, Parnassus
Contact: Adam Fries 415-476-4550 Adam.Fries@ucsf.edu

  • Imaris
  • Matlab
  • Metamorph
  • NIS Elements
  • Solidworks
Parnassus

DRC Microscopy Core

Diabetes Research Center, Parnassus
Contact: Adam Fries (415) 476-4550 Adam.Fries@ucsf.edu

  • Image Analysis Software