Technology Opportunities

Objective/function

• The Bioinformatics Unit provides consultation, education and computational services to the Hebrew University biological and medical research community

Research provided

• Genomic data analysis
• Sequence analysis
• Structural biology bioinformatics consultation
• Seminars
• Workshops

Advantages

• The Bioinformatics Unit has a highly knowledgeable, skilled staff utilizing state-of-the-art equipment and technologies

Client record

• Hadassah Medical Center
• HUJI researchers

Available equipment

Infrastructure

• New bioinformatics servers: COMBI and OMICS, SGI origin 300, with Irix operating system, connected to a 2 TB storage device

Software

• SRS 8.1, with EMBOSS functions embedded, as well as standalone EMBOSS. In addition to the command line SRS and EMBOSS, SRS may be used with a web interface
• Perl, as well as some modules of BioPerl.
• Other programs/packages: BLAST, ClustalW, Vienna Package, meme, mast

Databases

• Nucleotide: EMBL, REFSEQ nucleotides
• Protein: Niprot: Swissprot and TREMBL; PDB
• Domain: Prosite, PFAM and Prints
• Mutations: OMIM

Genomic Analysis

• Matlab and Perl-based dedicated custom-built server
• Special filters and other built image processing packages
• Statistical analysis, data normalization and clustering are carried out with several software packages: Spotfire, Acuity, Jsota, Genepix, ScanAyze, SAM
• Custom-packages built using Matlab and Perl
• Access to free packages such as Bioconductor or Afymetrix and other gene annotation tools

Structural Analysis

• DS Modeling 1.1 (Accelrys, Inc) molecular modeling programs with modules for
• Structural visualization and manipulation of biological molecules
• Model building using homology modeling (Modeler)
• Molecular dynamics and energy minimization calculations (CHARMm)
• Electrostatic calculations (GRASP)

Staff

• Tamar Kahan, PhD
• Yoav Smith, PhD

Contact

• Tamar Kahan, PhD, Bioinformatics Unit, tamar.kahan@huji.ac.il
• Yoav Smith, PhD, Genomic Data Analysis Unit, smith@md.huji.ac.il
• Link to homepage http://bioinfo.md.huji.ac.il/default.asp