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<div class="container">
<div class="row">
<div class="col-sm-6 col-md-3">
<h2>MetFragWeb</h2>
<h2>MetFrag Web</h2>
<p><a class="btn btn-primary" href="/MetFrag/projects/metfragweb" role="button">Learn more</a></p>
<p>Use <a href="https://msbi.ipb-halle.de/MetFrag/">MetFrag</a> directly from your browser for a visual,
interactive experience. Great for beginners or exploring your data</p>
Expand All @@ -26,7 +26,7 @@ <h2>MetFrag CL</h2>
</div>

<div class="col-sm-6 col-md-3">
<h2>MetFragR</h2>
<h2>MetFrag in R</h2>
<p><a class="btn btn-primary" href="/MetFrag/projects/metfragr" role="button">Learn more</a></p>
<p>Users familiar with R can download the <a href="https://github.com/ipb-halle/MetFragR">MetFragR</a>
R-package, or use MetFrag built into the <a href="https://rickhelmus.github.io/patRoon/">patRoon</a> workflow</p>
Expand All @@ -42,10 +42,14 @@ <h2>Converter</h2>

<h3>Overview</h3>

<p>MetFrag is a freely available software for the annotation of high precision tandem mass spectra of metabolites which
is a first and critical step for the identification of a molecule&#39;s structure. Candidate molecules
of different databases are fragmented in silico and matched against mass to charge values. A score calculated
using the fragment peak matches gives hints to the quality of the candidate spectrum assignment.</p>
<p>MetFrag is a freely available software to annotate metabolites and other small molecules using
fragmentation information from tandem mass spectra, which is a first and critical step towards
identification of a molecule&#39;s structure. Candidate molecules can be retrieved from
different databases using mass or molecular formula and are then fragmented in silico
and matched against the fragments. The resulting score calculated using the fragment peak matches
can be used to rank the various candidate molecules. Additional scoring terms, including an
experimental mass spectral library match, or database-specific scoring terms such as
patent and literature values can be defined in the settings. </p>

<h3>Availability</h3>

Expand All @@ -58,32 +62,46 @@ <h3>Availability</h3>
For R users, options include the <a href="/MetFrag/projects/metfragr">MetFragR R-package</a>
and the integrated non-target screening workflow <a href="https://rickhelmus.github.io/patRoon/">patRoon</a>.</p>

<h3>Publications</h3>
<h3>Citing MetFrag</h3>

When using MetFrag, please cite: </p>
<a href="http://jcheminf.springeropen.com/articles/10.1186/s13321-016-0115-9">MetFrag relaunched: incorporating strategies beyond in silico fragmentation</a>:
C Ruttkies, E L Schymanski, S Wolf, J Hollender, S Neumann
Journal of Cheminformatics 2016 8:3 </p>
<p>Please cite this article when using MetFrag: </p>
<p>C Ruttkies, EL Schymanski, S Wolf, J Hollender, S Neumann (2016)
<a href="https://doi.org/10.1186/s13321-016-0115-9">MetFrag relaunched: incorporating strategies beyond in silico fragmentation</a>
Journal of Cheminformatics 8:3. DOI: <a href="https://doi.org/10.1186/s13321-016-0115-9">10.1186/s13321-016-0115-9</a>
</p>

<p>MetFrag with fragment learning:</p>
<a href="https://doi.org/10.1186/s12859-019-2954-7">Improving MetFrag with statistical learning of fragment annotations</a>:
C Ruttkies, S Neumann, S Posch
BMC bioinformatics 20, 376</p>
<h3>Other MetFrag Publications</h3>

<p>MetFrag and HD Exchange:</p>
<a href="https://doi.org/10.1007/s00216-019-01885-0">Supporting non-target identification by adding hydrogen deuterium exchange MS/MS capabilities to MetFrag</a>:
C Ruttkies, EL Schymanski, N Strehmel, J Hollender, S Neumann, AJ Williams, M Krauss
Analytical and Bioanalytical Chemistry 411(19), 4683–4700</p>
<p><b>Exposomics - MetFrag Meets PubChemLite: </b>
EL Schymanski, T Kondic, S Neumann, PA Thiessen, J Zhang, EE Bolton (2021)
<a href="https://doi.org/10.1186/s13321-021-00489-0">Empowering large chemical knowledge bases for exposomics: PubChemLite meets MetFrag</a>
Journal of Cheminformatics 13:19. DOI: <a href="https://doi.org/10.1186/s13321-021-00489-0">10.1186/s13321-021-00489-0</a>
</p>

<p>Version 2010:</p>
<a href="http://www.biomedcentral.com/1471-2105/11/148/abstract">In silico fragmentation for computer assisted identification of metabolite mass spectra</a>:
S Wolf, S Schmidt, M Müller-Hannemann, S Neumann
BMC bioinformatics 11 (1), 148 </p>
<p><b>MetFrag with Statistical Fragment Learning:</b>
C Ruttkies, S Neumann, S Posch (2019)
<a href="https://doi.org/10.1186/s12859-019-2954-7">Improving MetFrag with statistical learning of fragment annotations</a>:
BMC Bioinformatics 20: 376. DOI: <a href="https://doi.org/10.1186/s12859-019-2954-7">10.1186/s12859-019-2954-7</a> </p>

These are the papers in
<p><b>MetFrag and HD Exchange:</b>
C Ruttkies, EL Schymanski, N Strehmel, J Hollender, S Neumann, AJ Williams, M Krauss (2019)
<a href="https://doi.org/10.1007/s00216-019-01885-0">Supporting non-target identification by adding hydrogen deuterium exchange MS/MS capabilities to MetFrag</a>:
Analytical and Bioanalytical Chemistry 411(19), 4683–4700.
DOI: <a href="https://doi.org/10.1007/s00216-019-01885-0">10.1007/s00216-019-01885-0</a> </p>

<p><b>MetFrag Relaunched (2016): </b>
C Ruttkies, EL Schymanski, S Wolf, J Hollender, S Neumann (2016)
<a href="https://doi.org/10.1186/s13321-016-0115-9">MetFrag relaunched: incorporating strategies beyond in silico fragmentation</a>
Journal of Cheminformatics 8:3. DOI: <a href="https://doi.org/10.1186/s13321-016-0115-9">10.1186/s13321-016-0115-9</a>
</p>

<p><b>Original MetFrag Version (2010):</b>
S Wolf, S Schmidt, M Müller-Hannemann, S Neumann (2010)
<a href="https://doi.org/10.1186/1471-2105-11-148">In silico fragmentation for computer assisted identification of metabolite mass spectra</a>:
BMC Bioinformatics 11:148. DOI: <a href="https://doi.org/10.1186/1471-2105-11-148">10.1186/1471-2105-11-148</a>.
Here are the papers that have cited MetFrag (version 2010) so far in
<a href="http://www.ncbi.nlm.nih.gov/pubmed?linkname=pubmed_pubmed_citedin&from_uid=20307295">PubMed</a>
and <a href="http://scholar.google.com/scholar?oi=bibs&hl=en&cites=10278388642349466161&as_sdt=5">google scholar</a>
that have cited MetFrag (version 2010) so far.
and <a href="http://scholar.google.com/scholar?oi=bibs&hl=en&cites=10278388642349466161&as_sdt=5">Google Scholar</a>. </p>

<h3>License</h3>

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<h3>MetFrag news</h3>
<ul class="news list-unstyled" >

<li><p><b>22 October, 2024 </b>New MetFrag Command Line version released. Grab <a href="https://github.com/ipb-halle/MetFragRelaunched/releases/tag/v2.5.1">MetFragCommandLine-2.5.1.jar</a> now!</p></li>
<li><p><b>18 October, 2024 </b>We are working on an updated MoNA library within MetFrag. Keep an eye on <a href="https://github.com/ipb-halle/MetFragRelaunched">MetFragRelaunched</a>.</p></li>
<li><p><b>18 October, 2024 </b>An updated MoNA LC-MS/MS library for MetFrag is now available on <a href="https://doi.org/10.5281/zenodo.13951787">Zenodo</a>.</p></li>
<li><p><b>08 March, 2021 </b>New publication about MetFrag and PubChemLite now avaialble at DOI: <a href="https://doi.org/10.1186/s13321-021-00489-0">10.1186/s13321-021-00489-0</a>.</p></li>
<li><p><b>05 March, 2019 </b>A Bayesian model has been included to improve the MetFrag annotation results. Find out more on <a href="/MetFrag/projects/metfragcl">MetFrag CL</a>.</p></li>
<li><p><b>28 April, 2016 </b>The MetFrag R package has been rebuilt and updated to version 2.0. Check it out on <a href="/MetFrag/projects/metfragr">MetFragR</a>.</p></li>
<li><p><b>10 July, 2015 </b> The new Metfrag commandline tool is available on our website. Check out <a href="/MetFrag/projects/metfragcl">MetFrag CL</a>.</p></li>
<li><p><b>23 November, 2014 </b> The <i>in silico</i> derivatised KEGG database is now available in the MetFragWeb beta version. </p></li>
<li><p><b>17 February, 2014 </b> The <a href="/MetFrag/projects/converter">converters section</a> is now published on the web site. </p></li>
<li><p><b>14 February, 2014 </b> Website goes online. </p></li>
<li><p><b>25 October 2024 </b>New MetFrag Command Line version released with updated MoNA library. Grab <a href="https://github.com/ipb-halle/MetFragRelaunched/releases/tag/v2.6.1">MetFragCommandLine-2.6.1.jar</a> now!</p></li>
<li><p><b>22 October 2024 </b>New MetFrag Command Line version released. Grab <a href="https://github.com/ipb-halle/MetFragRelaunched/releases/tag/v2.5.1">MetFragCommandLine-2.5.1.jar</a> now!</p></li>
<li><p><b>18 October 2024 </b>We are working on an updated MoNA library within MetFrag. Keep an eye on <a href="https://github.com/ipb-halle/MetFragRelaunched">MetFragRelaunched</a>.</p></li>
<li><p><b>18 October 2024 </b>An updated MoNA LC-MS/MS library for MetFrag is now available on <a href="https://doi.org/10.5281/zenodo.13951787">Zenodo</a>.</p></li>
<li><p><b>08 March 2021 </b>New publication about MetFrag and PubChemLite now avaialble at DOI: <a href="https://doi.org/10.1186/s13321-021-00489-0">10.1186/s13321-021-00489-0</a>.</p></li>
<li><p><b>05 March 2019 </b>A Bayesian model has been included to improve the MetFrag annotation results. Find out more on <a href="/MetFrag/projects/metfragcl">MetFrag CL</a>.</p></li>
<li><p><b>28 April 2016 </b>The MetFrag R package has been rebuilt and updated to version 2.0. Check it out on <a href="/MetFrag/projects/metfragr">MetFragR</a>.</p></li>
<li><p><b>10 July 2015 </b> The new Metfrag commandline tool is available on our website. Check out <a href="/MetFrag/projects/metfragcl">MetFrag CL</a>.</p></li>
<li><p><b>23 November 2014 </b> The <i>in silico</i> derivatised KEGG database is now available in the MetFragWeb beta version. </p></li>
<li><p><b>17 February 2014 </b> The <a href="/MetFrag/projects/converter">converters section</a> is now published on the web site. </p></li>
<li><p><b>14 February 2014 </b> Website goes online. </p></li>
</ul>

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