Corra v3.0 release in soureforage.
Mi-Youn Brusniak
Dear Corra users,
I am sending this email since either you are in corra google group list or you have contact me in the past with Corra request.
If you are in the both group with different email address, I apologize that you may get this email in both account or duplicates.
The following is an exception from Corra v3.0 release note from https://sourceforge.net/projects/corra/files/.
Please visit sourceforge.net website or http://tools.proteomecenter.org/Corra/corra.html for more detail information including software source code.
Corra is an open source project under Apache 2.0 license.
Warm Regards,
Corra Development Team.
Mi-Youn Brusniak,
Hector Ramos,
Mark Christiansen,
Sung-Tat Kwok,
Micheleen Harris
Computational Biology
Seattle Proteome Center
Tel: (206)732-1327
Corra v3.0
In ISB, we have continuously utilized Corra software for our biological studies since 2007. While we are applying Corra for various biological systems, we identified new features, modules and bugs that can meet our needs in our continuous research last three years. Some of Corra users contacted me separately to get updated version Corra v2.5 last year. Now, we have added many features and modules including many requests on “single CPU” processing capability, our team decided to release Corra v3.0 for our proteomics label free research community.
I listed the highlight changes that are included in Corra v3.0.
- Added processing steps after Statistical Analysis:
The “Inclusion List Builder” and “Target Feature Annotation” steps are added after “Statistical Analysis”.
Published Corra workflow* was ended in detecting differentially expressed features that are statistically significant. However, past two years we have been building the target features and using scheduled precursor target analysis LC-MS technique published by Alex Schmidt*. Thus, we have been routinely using “Inclusion List Builder” and “Target Feature Annotation” to identify the differentially expressed features.
- Beyond peptide analysis exploration:
After identify the peptides, researchers are often mapped to protein or gene identification along with quantification (log Fold Change) and statistical (log Odd) values in order to see their relationship in GO (Gene Ontology) annotation or HPRD (Human Protein Reference Database). Thus, Corra v3.0 has a way to deliver identified peptide to protein and gene connection with various visualization tools by using PIPE2 (Protein Information and Property Exploration 2)*.
- Added feature extraction and alignment tools:
In 2007, Corra had two feature extraction and alignment tools – SpecArray* and SuperHirn*. Similar to database searching algorithms, we don’t have very clear case of which feature extracting and alignment algorithms are working out consistently best for all type of biological samples and Mass spectrum machines. Thus, we have some LC-MS proteomics dataset that are used one or more tools to get the candidate differentially expressed features and peptide candidates. In Corra v3.0, we have added two additional such modules, msBID* and OpenMS*.
- Single thread application:
While we are fully utilizing distributed processing mechanism of Corra for > 30 LC-MS run processing (or even 100s) LC-MS run processing, several researchers from different organization asked whether we can provide “single thread application” that do not have “PBS” (portable batch system) or “SGE” (Sun Grid Engine) or “LFE” (Load Sharing Facility). Though such a code can be easily developed by extending an abstract convenience class org.systemsbiology.apps.corragui.server.job.JobManager as explained in previous Corra installation guide section H, we go ahead and added ShellJobManager and also added SunGridEngineJobManager to Corra v3.0. Please remember to configure Corra/CorraGui/trunk/conf/corra_webapp.properties file to have corra.scheduler.jobmanager.class= org.systemsbiology.apps.corragui.server.job.ShellJobManager. Please read new installation guide section H.
- Upgraded software platform and license:
We have upgraded our software to use GWT 2.0.4 from GWT 1.6 and tested in more secure version of Apache Tomcat-6.0.26. Thus, Corra v3.0 deploys more standard java community web components WAR format instead of webapp in Corra v2.0. Corra v3.0 is also free Open Source software under Apache 2.0 license.
- Updated installation instructions and instruction and latest source codes:
Updated installation instructions and instruction and latest source codes can be found in http://tools.proteomecenter.org/Corra/corra.html.
Source codes can be downloaded using the sourceforge link provided in the corra website. http://tools.proteomecenter.org/Corra/corra.html.
- Future release and additional features:
As we have more accumulated features that can be useful to community, we will release new versions. We are currently working on protein level quantification analysis modules that can be added for the next version.
We sincerely appreciate that you are interested in using Corra and thank you for your feedback on what modules might be useful. Sorry that we do not have resource to test out all Operating Systems and version to support some of unique issues but we will do our best to answer questions we can address.
“*” reference article is provided in release note.