Illinois Bio-Grid Developed Software

IBG GeneDesigner

IBG GeneDesigner is an open-source product available for free download. It is still in development, but it can be used to design a nucleotide sequence for a particular protein (amino acid sequence) such that it will be optimized for the highest possible expression when used as a recombinant DNA fragment in a particular organism.

• GeneDesigner is available via Java Web Start.
  • Simply click here to download and run the application over the web.

Download GeneDesigner v 4.10 which is integrated in the IBGDesktop by downloading the IBGDesktop at the link below

• Run it by typing at a command line:

java -jar IBGProteinDesktop.jar

• You can also (in Windows) just double click on the jar file.

• Manual and improvements to be forthcoming soon.

IBG DeskTop

IBG DeskTop is an open-source product available for free download. It is still in development, but it can be used to view Mass Spectra and can help to determine de novo sequence.

• Sample data files (below)

• Download latest version IBGDesktop.jar: IBG DeskTop v 4.10 (r2893, 05 Jan 2009; 1.47 MB)

• Older version : IBG DeskTop (r2804, 19 May 2008; 1.77 MB)

• Older version 0.90 IBG DeskTop v 0.90 (as of 15 August 2006; 9.1 MB)

• Older version 0.83 IBG DeskTop v 0.83 (Jul 12, 2005 273Kb)

Run it by typing at a command line:

For version 0.83 and 0.90

java -jar IBGProteinDesktop.jar

For version 0.92 and beyond

java -Xmx1024M -jar IBGDesktop.jar

You can also (in Windows) just double click on the jar file.

Manual and improvements to be forthcoming soon.

IBG High Throughput Task Allocator

This library addresses the problem of searching huge biological databases on the scale of several gigabytes by utilizing parallel processing. Biological databases storing DNA sequences, protein sequences, or mass spectra are growing exponentially. Searches through these databases consume exponentially growing computational resources as well. The library provides a general use, MPI based, C++ framework for generically splitting databases amongst several computational nodes. The combined RAM of the nodes working in tandem is often sufficient to keep the entire database in memory, and therefore to search it efficiently without paging to disk. The framework runs as a persistent service, processing all submitted queries. This allows for query reordering and better utilization of the memory. Thereby, it achieves superlinear speedups compared to single processor implementations. The library is the basis for searches in the IBG Mass Spectrometry Database.

The HTTA is a general use framework intended for use by any database searching algorithm. The database searching algorithm must be placed in a plug-in module with the specified API. We show two real implementations in our two concomitant projects that search a Mass Spectrometry database of empirically derived spectra. These projects are the k-similarity search and the cosine similarity search. Both projects are available on this page.

Details about the program can be found in Dominic Battre's Master's thesis "Distributed Searching in Biological Databases". The source code and doxygen comments can be found at http://histone.rrc.uic.edu/mpitf/.

The most current version can be found in subversion at https://histone.rrc.uic.edu/mpitf/.

Source Code:

You can download the source code for the most current version at http://histone.rrc.uic.edu/mpitf/download/mpitf-0.2.tar.gz. You can download the generated doxygen documentation from http://histone.rrc.uic.edu/mpitf/download/html.tar.gz

Documentation:

You can browse the doxygen web page documentation at http://histone.rrc.uic.edu/mpitf/doxygen/html/index.html.

Search the Empirical Database of Mass Spectra:

You can use the HTTA to try to identify your protein or peptide with our database of empirically derived Mass Spectra at http://histone.rrc.uic.edu/IBG-MSP-domi/. You can see it in action with a plug-in that performs either a k-similarity search on Mass Spectra on a large database of empirically derived proteomic spectra or that performs a cosine similarity search on that same database. http://histone.rrc.uic.edu/svn/taskfarmer/trunk/mpitf/src/examples/ibgsc/

Explanation of Searching Algorithms

• Spectral Comparison
  • Spectral Comparison uses cosine similarity and the similarity index to compare mass spectra.
  • The spectral comparison paper is available from http://ericpuryear.com/spectral-comparison-puryear.pdf

• K-mutation Spectral Similarity Algorithms
  • The K-mutation algorithm takes an experimental spectrum and searches the database for a spectrum that is the best match among spectra that are at most k mutations or modifications apart from the database spectra
  • The following is a link to a paper that describes the implementation of the K-mutations algorithm, cosine similarity algoritm, and similarity index algorithm integrated together as a protein identification search engine. http://gridweb.rrc.uic.edu/twiki/pub/Main/HussamAlaEldeen/Implementing_Spectral_Similarity_fasttrack.pdf
  • TODO: where to download
    • stand-alone library version
    • HTTA plug-in version
  • TODO: where to find it in Subversion
  • The following is a link to where you can find generated javadoc files: http://histone.rrc.uic.edu/mpitf/doxygen/html/namespaceIBGSC.html#7b1d4500953e6d227f9b3c5541f815ee
  • The link to the website where experimental spectra could be submitted for identification is: http://www.illinoisbiogrid.org/MSDB/

IBG Workbench Libraries

• Many experiments in the field of Proteomics are hypothesis driven where researchers are searching for answers to specific questions. Many of the current Mass Spectrometry (MS) analysis utilities are insufficient for use in analyzing such hypothesis driven experiments (HDEs). The IBG Workbench is a set of C shared libraries, among other things, that allow for rapid development of utilities intent on analyzing Proteomic MS HDEs. The IBG Workbench allows abstraction of common Proteomic and MS data types, I/O routines and fundamental MS analysis processes that allow programmers to focus on the biologically significant programming logic of their analysis utilities rather than the tedious tasks of data structure design and I/O functionality.

• Project Home
• Download Current IBG Workbench Release
• Subversion Development
• Documentation

IBG Inverse Folding Project

• The IBG Inverse Folding Project is currently exploring a variety of methods that may be used to design an appropriate amino acid sequence for a protein given only it's three dimensional backbone structure. Current techniques include nearest neighbor effects, phi/psi probabilities, pairwise distance propensities, and others. The project is currently in development and the source code changes constantly. However, interested students may download the code from the subversion service below. The code is written is C and is meant to be available to many computationally intense protein specific applications.

• http://histone.rrc.uic.edu/svn/

• Coming soon, a grid enabled inverse folding application for your web browser

IBG Rama Map

• The IBG Rama Map is a utility to allow researchers to visualize the Ramachandran distribution of phi/psi angles. The IBG Rama Map allows researchers to select single amino acids, and to include nearest neighbors effects. Furthermore, the researchers may select portions of the map to examine more thoroughly for amino acid distributions.

• To try the full downloadable version simply click here to download and run the application over the web. Run the program as described above under IBG designer.

• Try a simpler version on line at http://www.illinoisbiogrid.org/RamaMap

IBG Bioinformatics Interactive Programming Environment

Advancements in the field of bioinformatics require expertise in both molecular biology and computer science. Few can claim to be masters of both. Too often, during the software development stage of a bioinformatics project, computer scientists struggle to include the relevant biological data, or molecular biologists ignore common computer science techniques and principles. Software written under such constraints either lack the expressiveness required for molecular modeling and experiments or otherwise fails to provide reusable code and the value of the software is therefore limited to a narrow task. The Illinois Bio-Grid Bioinformatics Interactive Programming Environment is a modular extensible open source software package envisioned and supervised by a collaboration of researchers with domain specific knowledge in both the biological and computer sciences. As such, the aim is to provide the bioinformatics community with the basic tools necessary to undertake molecular modeling projects without undertaking the costly and time consuming process of software development.

Documentation:

You can browse the doxygen web page documentation at http://histone.rrc.uic.edu/bipe/html/index.html.

IBG Digital Lab Notebook

The IBG Digital Lab Notebook is a collaborative project with the Field Museum creating a web based record keeping and project management utility for multi-user PCR experiments.

Sample MS Data Files:

• Right click to save to your local computer or click to view their text format:
  • BSA_Trypsin_51115BSA_pept0003.mgf: MGF-Standard (835 KB)
    • Ion Trap run of tryptic peptides from bovine serum albumin courtesy of Don Wolfgeher, Univ. Chicago
  • largeFTMS.mzXML: Large (~7 MB) mzXML file from FT MS experiment
    • May require extra memory to open
    • Recommended settings (download IBGProteinDesktop.jar): java -jar -Xms256m -Xmx512m IBGDesktop.jar

Pseudo OOP Methods in C

Example of coding technique to introduce Object Oriented like concepts into C. Pseudo OOP Methods in C.

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-- DaveAngulo - 05 Jan 2009
-- DaveAngulo - 05 Mar 2008
-- DennisBergau - 16 October 2006
-- LarryHelseth - 05 Sep 2006
-- LarryHelseth - 30 Aug 2006
-- DaveAngulo - 05 Mar 2006
-- KevinDrew - 03 Mar 2006
-- TWikiGuest - 30 Dec 2005