Illinois Bio-Grid Projects

Possible future Bio-Grid projects are listed on the ideas page.

Mass Spectrometry

IBG Software

• Mass Spec Database
• Additional project ideas for the Mass Spec Database
• Annotations editor and structured Annotations XML
• IBG Mass Spectrometry Workbench
  • Mass Spec Desktop
  • Mass Spec Data Management
  • Mass Spec Hydrogen-Deuterium Exchange Rate Calculator
  • Mass Spec Peptide Spectral Matcher
  • Simple Cosine Similarity Spectral Comparicon
  • k-Mutation Spectral Alignment
• Known Modification Quantification Tool
• High Throughput Molecular Screening Library Assistant
• Molecular Screening Library documentation and notes
• Mass Spectrometry Desktop - Visualization and Annotation

3rd-Party Tools

• Lutefisk a de novo analysis tool
• OMSSA a sequence database searching tool
• Mascot a sequence database searching tool
• X!Tandem a de novo analysis tool
• Clustering and Alignment Tool (CAT) a program which analyzes (Screens, clusters and aligns) the DNA sequence data (DoubleTwist)
• ClustalW program for protein sequence analysis
• GenScan command line program for gene identification
• GCG Wisconsin Package software for comprehensive sequence analysis.
• Hmmer program for protein sequence analysis
• Pblast parallel/distributed BLAST server
• Prophecy search application to find data in the Annotated Human Genome Database

Proteomics

IBG Software

• Gene Designer. A tool that takes an amino acid sequence and calculates the best nucleotide sequencce for PCR that will produce the best expression, especially when restriction enzymes are taken into account.
• Ramachcandran Map Viewer. A tool that will show Ramachandran maps with various criteria
• Inverse Folding Tool Jon Gemmell needs to write a description.
• Kah. A tool written in Python originally implemented at Argone National Laboratories which is used to load and access mass spectrometry experiment results.

Infrastructure

IBG Software

• High Throughput Task Allocator for database searching

3rd-Party Tools

• Bio-Grid Job Scheduling and Resource Management
• IBG Portal Development
• Grid Environment and Access

Phylogenetics

IBG Software

• _TODO: add the python app *

3rd-Party Tools

• MrBayes
• PAUP*
• PhyML

-- RobVogelbacher - 07 Jul 2005
-- DaveAngulo - 25 Sep 2005