MassChroQ

MassChroQ (Mass Chromatogram Quantification) is a free software (released under the Gnu General Public Licence version 3) for quantification of data obtained from Liquid Chromatography - Mass Spectrometry techniques.

MassChroQ performs alignment, XIC extraction, peak detection and quantification of LC-MS data. It is written in C++, has a Qt Graphical User Interface and is optimised for running smoothly on very large mzXML or mzML data on a desktop computer in a short time. It also offers paralelization for running in clusters and high performance computing facilities.

MassChroQ uses and produces only data in open standard formats (mxXML, mzML, gnumeric, csv etc.) It also accepts an on-purpose defined XML format called masschoqML, which offers the possibility of easily embedding MassChroQ's input or ouput in third party software. For example, MassChroQR is an R package processing masccroqML data for statistical analysis. Also, the X!Tandem pipeline's identified peptides can be automatically integrated into the masschroqML input file.

MassChroQ is available for download for several operating systems, including a Debian based package.

See the MassChroQ homepage for further documentation or the MassChroQ project on the SourceSup forge for development needs.

I worked with MassChroQ from 2009 until 2012, and I brought the project from a C++ home made prototype to its fully functional releasable state (releases 1.X until 2.0). During this period I was the main core developer, but I would have done nothing, not even a single thing, without the collaborative wonderful work of my development supervisor and mentor Olivier Langella, our team chief Michel Zivy and the naturally born hacker Benoit Valot. The project also benefited from the valuable help of our postdoctoral researchers Ludovic Bonhomme and Melisande Blein, who tested in real-time and pushed MassChroQ to its limits.

Databroker

Databroker is a proprietary Message Oriented Middleware software edited by Telino. My work for Databroker consisted in building a C++ prototype of the software using the open source Apache Qpid messaging tools that follow the AMQP open internet protocol for reliably sending and reciving messages. I left the project shortly after the prototype was successfully tested and accepted. Since then I am convinced that whenever there is a proprietary software, there is an open source (thus better) alternative :)

Gene-regulation

Gene-regulation is a program written by Claire Rioualen in snakemake, for producing workflows for the analysis of Next Generation Sequencing data related to gene regulation (ChIP-seq, RNA-seq and related technologies).

My work with gene-regulation consists of implementing new workflows for analysing RNA-sequenced and Chip-sequenced data for the Calanques Bioinformatics Core Facility at TAGC and IBDM in Luminy, Marseille. These workflows are using python, shell and R scripting embedded in the snakemake workflow models provided by gene-regulation. During this work I am often modifying and adapting part of the original gene-regulation code.

MitoXplorer

MitoXplorer (to be published soon) is a web-based tool providing visualisation and analysis of large-scale expression and mutation data integrated with the mitochondrial interactome and pathways. The tool performs NGS-data analysis, extracts mutations and expression data for all mitochondria-localized proteins and integrates it with a curated mitochondrial interactome. One can then visualize changes in different experimental conditions and perform statistical analysis on them.

MitoXplorer is a collaborative project written in javascript, php and Python. My work in MitoXplorer consists in maintaining the GitLab project, supervising and helping with the git repository, help solving programming issues and debugging code if necessary. I am also supervising the internship development work on the project.