MaDada
MaDada is an open platform for bringing and facilitating FOIA (Freedom Of Information Access) requests to anyone. Freedom of information access is a fundamental right in numerous countries, and in most of them, as in France, it is also a constitutional right. MaDada is a project of Open Knowledge France.
MaDada is based on the free open-source software Alaveteli, which is deployed in numerous other countries worldwide, the way MaDada is in France : WhatDotheyKnow in the United Kingdom, Transparencia in Belgium, or AskTheEU pour FOIA requests towards the European Union.
Alaveteli platforms allow anyone to make FOIA requests towards a public administration (public agency, town hall, ministry, public company, etc), which has therefore the obligation to respond and transmit the documents, except in a few rare cases, as well as make them available in open data to the public. It is what is called the right to know, and the duty of public administrations to transparency towards its citizens (us). You should try it, it is simple to use. But do not expect answers to always arrive, this right being little respected by France and other countries, all the more reason to assert it more.
I worked for Open Knowledge France in the MaDada project, and in particular for coordination, technical development, user support, documentation, advocacy and community organizing, from 2020 until 2023.
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.