About the Illinois Bio Grid Click here for a 32 Mb avi file Mission Statement The Illinois Bio Grid is a consortium ...

This is a temporary page, it shall be merged with the tutorial once it is finished. After posting the message to the list, I realized that I was missing all the important ...

Name: Brian Jurries UserName: BrianJurries Email: Brian.Jurries@gmail.com Cell: 806 239 7439 BrianJurries 26 Jan 2006

PatrickSmyth 24 Sep 2006 The following code example was presented at the BioInformatics weekly research meeting held on September 18, 2006 as an example of a coding ...

by: Kevin Drew This algorithm takes in a Sequence and a !SeqTag and returns a list of possible sub sequences A Sequence might look something like this: A B C D E F ...

This page is for documentation on the !ComputeSequenceDerived BandY ionSpectrum algorithm KevinDrew 20 Jan 2005 ComputeSequenceDerived BandY ionSpectrum: ...

Digital Lab Notebook Overview The IBG Digital Lab Notebook is a collaborative project with the Field Museum creating a web based record keeping and project management ...

Molecular Screening Library Documentation User Documentation MaldiQuantifierUserDoc MaldiPTMFilterUserDoc Requirements for individual tools MaldiPTMFilter ...

EricPuryear 13 Jul 2005 NOTE: this and the paper are now in subversion in /svn/papers/epuryear Please use that copy. Enhancing the Mass Spectrometry I/O Framework ...

Sources of funding The following are the sources of funding for this project: National Institutes of Health This work was funded in part by the National ...

GeneDesigner Overview The IBG !GeneDesigner is a component of the IBG Protein Desktop application which can be used to generate a DNA sequence from a given protein ...

This is how to get accounts for the various resources of the Illinois !BioGrid Subversion Follow SubversionAccount gridweb.cti.depaul.edu Ask EricPuryear histone ...

Getting Started With Linux If you have never used Linux we recommend using the Linux computers in the lab. They are nicely set up. If you prefer using your windows ...

Grid Environment Placeholder to keep track of information about Globus install on z cluster and IBG Hardware Installation Notes RJV 10.26.06: ...

Picture of many of the group members on March 20, 2006. From left: Mike Boyle, Rob Vogelbacher, James Didier, Bryan Beaumont, Greg Zivich (in back), Renee !MacElhaney ...

Illinois Bio Grid Hardware Z Cluster The z cluster is an high performance Linux cluster installed at the School of Computer Science, Telecommunications and Information ...

Histone Subversion not responding Issue Subversion fails to respond on the web. Observations Numerous apache processes are running and has exceeded the number ...

Illinois Bio Grid System Access Please contact Dave Angulo for access to the IBG computational resources. Subversion Instructions for obtaining a Subversion ...

News about the Illinois Bio Grid Link Date Description NCBI AGENDA tentative.doc October 4 6, 2006 CTI Co hosting NCBI bioinformatics mini cources http://www ...

Illinois Bio Grid DePaul Bioinformatics Group People Primary Investigator Dave Angulo Students Below is a list of the students working on this project. What ...

Illinois Bio Grid Portal Development Overview Portal Technologies The following comparison of portlets vs servlets came from a !JavaZone presentation by Oliver Koeth ...

Illinois Bio Grid Projects For an overview of our current research investigations, please see Research Areas. Possible future Bio Grid projects are listed on the ideas ...

Illinois Bio Grid DePaul Bioinformatics Group Publications The following documents have been published as part of the research associated with the Illinois Bio ...

Illinois Bio Grid DePaul Bioinformatics Group Research Areas Genomics Genomics is the field of investigating proteins based on their primary structure (DNA nucleic ...

IBG Services These are the services on our web sites that IBG performs using our computational resources without charge. IBG Web Prot Id To see what this web service ...

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 ...

Sunfire Storage Array Configuration Overview The Sunfire 68K which comprises titan and myosin is connected to a Sun enterprise !StorEdge T3 storage array cabinet ...

Illinois Bio Grid System Topology The following diagrams describe the current computational environment of the IBG Z Cluster (kdrew: this graphic is outdated ...

Illinois Bio Grid Glossary Our own wikipedia of bioinformatics and grid terms Also see Other BioInformatics glossaries BioInformatics Glossary $ ab initio ...

Illinois Bio Grid Job Scheduler Proposal Goals Install and configure a freely available job scheduler on z cluster and Illinois bio grid computers for automated job ...

EricPuryear 03 Aug 2006 Compute nodes won't boot without a keyboard or KVM switch plugged in. After total power loss, nodes may not NFS mount the /maxtor300gb ...

JenniferVanPuymbrouck 13 Jul 2005 Mass Spec Database Paper Outline 1) Abstract 2) Introduction a. Overview of what will be presented b. Brief background ...

http://gridweb.cti.depaul.edu/twiki/bin/view/Main/GilKwak GilKwak 03 May 2006

KevinDrew 10 Jan 2006 Maldi PTM Filter Modification detection/quantification in samples with unknown modified and unmodified peptides Workflow: 1. MS run on ...

LaurieParker 16 Feb 2006 Maldi PTM Quantifier Tool for quantifying degree of modification in Maldi mass spectra, designed around phosphorylation and thiophosphorylation ...

IBG Maldi Quantifier User Documentation The IBG Maldi Quantifier tool is for quantifying the degree of modification in Maldi mass spectra. It was developed around ...

Project Description Project Members Dave Angulo Dominic Battre Hussam Ala Eldeen Eric Puryear Jennifer Von Puymbrouck Rob Vogelbacher ...

Project Ideas for the Mass Spec Database Delete operations For testing it would be very handy to have a means to delete accessions, mass specs, or peak annotations ...

Parser strategies for the Mass Spec Projects Bold items are those which have found a consensus. Parsers RAP: allows fast indexing, works for ...

IBG Workbench Project Description This project entails developing solutions for anaylsis of Mass Spectrometry data. This includes analysis tools such as !SpectralMatch ...

Mass Spectrometry Desktop Visualization Annotation Project Team members Marc Peters Gil Kwak Mariellen Dwyer Ben Cheung Mike Boyle Tracks ...

ReneeMcElhaney 30 Apr 2006

Minutes of Illinois Bio Grid Meetings Query Existing Action Items based on: MeetingMinutesTemplate Change ...

Meeting Minutes of Illinois Bio Grid, 06 Jul 2005 Attendees KevinDrew, RobVogelbacher 1. Discussion Topics Web Content We need to consolidate our three ...

Meeting Minutes of Illinois Bio Grid, Attendees Main., Main., Main., Main. 1. Action Item review 2. 3. Action Items !! NOP%{ who "TWikiGuest ...

MPI Debugging Debugging an MPI application can be pretty challanging: Processes can die from signals (Null Pointer Exceptions, Division by Zero, ...) without ...

MySQL can be found here: http://mysql.com MySQL documentation can be found here: http://dev.mysql.com/doc/

How to Setup a Project for Nightly Build Nightly build is also known as continuous integration or automated build. The nightly build application that is employed for ...

OpenConf can be found here: http://www.zakongroup.com/technology/openconf.shtml OpenConf documentation can be found here: http://www.zakongroup.com/technology ...

by: Kevin Drew This is documentation for the HDX mass spec project. What follows is specifications for what needs to be done to computationally analyze mass spec ...

Illinois Bio Grid DePaul Bioinformatics Group List of Meetings in Proteomics Journal PAPER CALLS, CONFERENCES, and TALKS Archived Paper calls are available ...

PAPER CALLS ARCHIVED Please click on the header to sort. Paper Call Listings Name of Conference Location and Date of Conference URL Paper ...

This page is for collaborating on the Peptide Spectral Matcher project. Documentation OverviewMatch ComputePossibleSubSequences ComputeSequenceDerivedBandYIonSpectrum ...

Project ideas for Phylogenetics Parallel Version of Mesquite and P4 Mesquite and P4 are phylogenetic software packages in Java and Python. Both are pretty big but ...

Introduction With the completion of the Human Genome Project many biology research questions have turned to understanding the human proteome. A proteome is the set ...

Bio Grid Project Ideas Folding IBG Data Model Entry level Contribute to the IBG data model for proteins, including the read/write functions for outside formats ...

Project Tasks MSIOP mzXML reader (due 7 6 05, Eric, Done) mzXML writer (due 7 8 05, Eric, Done) licensing lgpl? apache? sourceforge project ...

Query Action Items in IBG Web WikiName: Topic name: State: open late closed Due Within: days " state "" within "" topic ...

Random Walk Framework Intra Chain Electron Transfer in Polypeptides DaveAngulo 10 Sep 2007 length 5 distribution.xls: Site frequency distribution, cubic lattice ...

Random Walk Framework Intra Chain Energy Transfer in Polypeptides DaveAngulo 10 Sep 2007

PatrickSmyth 24 Sep 2006 The following code scheme was articulated in order to implement a MVC architecture into the R code associated with the Pelagic application ...

R and PARAFAC R If you want to get ANYWHERE using this package, I ( GeorgeSteinhardt) would STROGNLY suggest searching this site: http://tolstoy.newcastle.edu.au ...

Illinois Bio Grid Random Walk Framework Particles suspended in solution undergo random movement in time and space (taken as continuum variables) that is often referred ...

Illinois Bio Grid DePaul Bioinformatics Group IBG Reading List This page is a list of papers, books, and other material that are useful for computer scientists ...

Job Scheduler/Resource Manager Evaluation Schedulers Evaluated Condor PbsPro Sun Grid Engine Torque Analysis All of the schedulers that were ...

This page is for documentation on the ScoreSequenceDerivedSpectrumAgainstExperimentalSpectrum. KevinDrew 20 Jan 2005 ScoreSequenceDerivedSpectrumAgainstExperimentalSpectrum ...

ToriHuang 11 Dec 2006

How to create an account 1. log on to z login.cti.depaul.edu with ssh 1. execute htpasswd2 n $USER to create a hash value of your password 1. Copy the ...

Sun Grid Engine Installation and Configuration Documentation Sun's Documentation is available from their docbook site here. Further information detailing ...

Systems Administration This page is a compilation of systems administration procedures and short cuts. Machines which have a specific item not available on the other ...

Dominic is working for his thesis on a framework that allows for buzzwordmode data locality aware high throughput task farming for database sequence searches /buzzwordmode ...

MariellenDwyer 03 Dec 2006

Timeline Milestones kdrew: I've updated some of the dates to reflect the actual start date 1. Design and prototype replicate analysis, averaging of modes, should ...

Illinois Bio Grid DePaul Bioinformatics Group IBG Tutorial (Training Guide) This document is a proposal for student training in the technologies required to perform ...

Illinois Bio Grid Wiki Click here for a 32 Mb avi file Welcome Welcome to the wiki home of the Illinois Bio Grid ...

Illinois Bio Grid DePaul Bioinformatics Group IBG Index See also the faster WebTopicList

" warn "off"}% Site Map Web Home About the IBG News Research Areas Publications IBG Software GeneDesigner ...

Illinois Bio Grid DePaul Bioinformatics Group IBG Notification Subscriptions This is a subscription service to be automatically notified by e mail when topics ...

IBG Web Preferences The following settings are web preferences of the IBG web. These preferences overwrite the site level preferences in ., and can be overwritten ...

TWiki's IBG web /view/IBG The IBG web of TWiki. TWiki is a Web Based Collaboration Platform for the Corporate World.

Illinois Bio Grid DePaul Bioinformatics Group IBG Search

Statistics for IBG Web Month: Topic views: Topic saves: File uploads: Most popular topic views: Top contributors for topic save and uploads ...

See also the verbose WebIndex.

Installation Decisions of Meeting on 11/22/05 OS: Debian latest stable (in favor of Red Hat because we are familiar with it and it has good maintenance features with ...

How to use the Z cluster The Z cluster was built with DCC which installs Torque. Torque is built on PBS, which is probably the most used resource management tool ...