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Finnee2016 is a Matlab toolbox that is being designed for analytical separation techniques hyphenated with high-resolution mass spectrometry (X-HRMS). Finnee2016 is not a software; it is a collection of classes and functions that allow reading MS scans from mzML files and filter and transforms the data to visualise better the information. As any Matlab toolboxes, Finnee2016 cannot be used without a working Matlab session. Finnee2016 is compatible with Matlab2016a, some of the functions may also work using older versions. While a basic knowledge of Matlab is needed, no advanced programming skills are necessary. Operations are run by entering the correct line in Matlab command panel. If you are interested in testing Finnee but do not own a copy of Matlab, you can try contacting Mathworks and ask for a trial. They are also plenty of Matlab tutorial for beginners in YouTube.
Commercial instruments come with software that allows analysing (X-HRMS) dataset, so what is the point of developing or learning a new tool? Commercial software are often designed for mass spectrometer used as standalone instruments and do not fully take advantage of the separation dimension. Chemometrics and bioinformatics applied to X-HRMS information are a very dynamic field. Excellent software such as xcms and mzMine2 are increasingly being used. The aim of FInnee2016 is not to copy them using another language. Finnee2016 is specifically designed for high-resolution mass spectrometry with MS1 experiment and is not specific to a particular field. Moreover, Finnee2016 ambitions to provide a comprehensive analysis from a single dataset. The fundamental approach is to extract relevant and accurate data that correctly described the results of the separation.
Finnee2016 is not a finished product. It is in constant development.Files are likely to be modified. Finnee2016 aims to be a collaborative work; you can correct, comment or contact me if you would like some unique features. You can also contact me or follow this project via Research Gate.
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POCI-01-0145-FEDER-006939 (Laboratory for Process Engineering, Environment, Biotechnology and Energy – UID/EQU/00511/2013) funded by the European Regional Development Fund (ERDF), through COMPETE2020 - Programa Operacional Competitividade e Internacionalização (POCI) and by national funds, through FCT - Fundação para a Ciência e a Tecnologia.
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NORTE‐01‐0145‐FEDER‐000005 – LEPABE-2-ECO-INNOVATION, supported by North Portugal Regional Operational Programme (NORTE 2020), under the Portugal 2020 Partnership Agreement, through the European Regional Development Fund (ERDF).
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IF/00528/2013, supported by FEDER funds through the Operational Programme for Human Potential and by National Funds through FCT - Foundation for Science and Technology.
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The Laboratory for process Engineering, Environment, Biotechnology and Energy (LEPABE), my host institution.
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The Laboratory of foodomics from Madrid, especially Professor Alejandro Cifuentes, Dr Carolina Simó and Tanize dos Santos Acunha.
Every file in the Finnee2016 repository, including this wiki, are copyrighted
BSD 3-Clause License
Copyright (c) 2016, Guillaume Erny All rights reserved.
Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
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Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
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Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
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Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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