Open Source Python Bio-Informatics Software

In Systems Biology models are created in various formats (Matlab, Java, C/C++, Python, ...). "Annotate Your Model" will help you to link your model to biological web resources by creating a CSV file containing MIRIAM annotations.

FreePM is an opensource physicians practice management / electronic medical record application. The company providing support for FreePM nolonger exists. You may consider TORCH http://sourceforge.net/projects/op-torch/ or one of the other FOSS EMR's.

This project incorporates a suite of tools that aim to allow researchers within Griffith's Imaging and Image Analysis Facility (GIIAF) to efficiently and effectively provide secure, centralised, web-accessible data storage, management and manipulation. The open-source Java-based OMERO software was customised to provide most of the features of this project.

Solving genetic algorithms in a distributed processing system. Developed in python with sockets.

LymPHOS2 is a web-based Application at www.LymPHOS.org containing peptidic and protein sequences and spectrometric information on the PhosphoProteome of human T-Lymphocytes. - Nguyen, TD., Vidal-Cortes, O., Gallardo, Ó., Abian, J., Carrascal, M., LymPHOS 2.0: an update of a phosphosite database of primary human T cells. Database 2015, 2015. DOI: 10.1093/database/bav115 - Carrascal, M., Ovelleiro, D., Casas, V., Gay, M., Abian, J., Phosphorylation analysis of primary human T lymphocytes using sequential IMAC and titanium oxide enrichment. J. Proteome Res. 2008, 7, 5167-5176. DOI: 10.1021/pr800500r - Ovelleiro, D., Carrascal, M., Casas, V., Abian, J., LymPHOS: design of a phosphosite database of primary human T cells. Proteomics 2009, 9, 3741–3751. DOI: 10.1002/pmic.200800701 - Gallardo, Ó., Ovelleiro, D., Gay, M., Carrascal, M., Abian, J., A collection of open source applications for mass spectrometry data mining. Proteomics 2014, 20, 2275-2279. DOI: 10.1002/pmic.20140012

A univariate and multivariate analysis UI. This project is no longer under development. Please use as you wish.

RStatServer is a system for quickly developing and deploying web applications that integrate statistical computations and graphics. It is built using the Zope web application develeopment system and the open-source statistical data analysis environment R

TCellXTalk is a comprehensive database of experimentally detected phosphorylation, ubiquitination and acetylation sites in human T cells. The web-app at www.TCellXTalk.org makes TCellXTalk accessible from Internet, and enables the in silico prediction of potential co-modified peptides to facilitate their experimental detection, using targeted or directed mass spectrometry, for the study of protein post-translational modification cross-talk. More detailed information on TCellXTalk and the people at the CSIC/UAB Proteomics Laboratory behind it can be obtained at https://www.tcellxtalk.org/about/ - Casanovas, A., Gallardo, Ó., Carrascal, M., Abian, J., TCellXTalk facilitates the detection of co-modified peptides for the study of protein post-translational modification cross-talk in T cells. Bioinformatics 2019, 35-8, 1404–1413, DOI 10.1093/bioinformatics/bty805 ( https://doi.org/10.1093/bioinformatics/bty805 )

pyMantis is a data-management system for (systems) biology build on the web2py framework. It features: tree based file explorer, relational db table wizzard with automated creation of user interfaces, internal and external access management, wiki, ..