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xieguigang committed Feb 22, 2024
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Expand Up @@ -651,7 +651,7 @@ <h2>Runtime &amp; System Requirements</h2>
</p>

<p>
MZKit workbench supports Windows 10/11 64Bit system and Windows Server 2016/2019.
MZKit workbench supports Windows 10/11 64Bit system and Windows Server 2016/2019/2022.
</p>

<p>
Expand Down Expand Up @@ -694,19 +694,33 @@ <h2 class="title text-center">License &amp; Copyright</h2>
analysis and data visualization. (2022) doi:<a
href="https://explore.openaire.eu/search/software?pid=10.5281%2Fzenodo.4603277">10.5281/zenodo.7040586</a>.

<br />

<ul>
<li>mzkit on ELIXIR biotools: <a href="https://bio.tools/mzkit">https://bio.tools/mzkit</a></li>
<li>mzkit on SciCrunch: <a
href="https://scicrunch.org/resources/data/record/nlx_144509-1/SCR_023936/resolver?q=SCR_023936&l=SCR_023936&i=rrid:scr_023936">RRID:SCR_023936</a>
</li>
</ul>
<br />
<ul>
<li>
MZKit® is a registered trademark of BioNovoGene Corporation, protected by copyright law and
MZKit® is a registered trademark of BioNovoGene Corporation, protected by copyright law
and
international treaties.
</li>
<li>
RawFileReader reading tool. Copyright © 2016 by Thermo Fisher Scientific, Inc. All rights
RawFileReader reading tool. Copyright © 2016 by Thermo Fisher Scientific, Inc. All
rights
reserved.
</li>
<li>
MS-DIAL was launched as a universal program for untargeted metabolomics that supports multiple
instruments (GC/MS, GC/MS/MS, LC/MS, and LC/MS/MS) and MS vendors (Agilent, Bruker, LECO, Sciex,
Shimadzu, Thermo, and Waters). Part of the spectrum algorithm in MZKit is developed based on the
MS-DIAL was launched as a universal program for untargeted metabolomics that supports
multiple
instruments (GC/MS, GC/MS/MS, LC/MS, and LC/MS/MS) and MS vendors (Agilent, Bruker,
LECO, Sciex,
Shimadzu, Thermo, and Waters). Part of the spectrum algorithm in MZKit is developed
based on the
<a href="http://prime.psc.riken.jp/compms/msdial/main.html">MS-DIAL project</a>.
</li>
</ul>
Expand Down Expand Up @@ -745,7 +759,8 @@ <h3 class="title">MIT License</h3>
<h3 class="title">Reference</h3>

<p>
The development of the MZKit workbench library based on these works, you are also can cite these
The development of the MZKit workbench library based on these works, you are also can cite
these
works if you use MZkit software:
</p>

Expand All @@ -756,51 +771,63 @@ <h3 class="title">Reference</h3>
Metabolomics, Nature Communications, 2019, 10: 1516.
</li>
<li>
Li S, Park Y, Duraisingham S, Strobel FH, Khan N, et al. (2013) Predicting Network Activity from
Li S, Park Y, Duraisingham S, Strobel FH, Khan N, et al. (2013) Predicting Network
Activity from
High Throughput Metabolomics. PLOS Computational Biology 9(7): e1003123.
https://doi.org/10.1371/journal.pcbi.1003123
</li>
<li>
Pang, Z., Chong, J., Zhou, G., Morais D., Chang, L., Barrette, M., Gauthier, C., Jacques, PE.,
Pang, Z., Chong, J., Zhou, G., Morais D., Chang, L., Barrette, M., Gauthier, C.,
Jacques, PE.,
Li, S., and Xia, J. (2021) MetaboAnalyst 5.0: narrowing the gap between raw spectra and
functional insights Nucl. Acids Res. (doi: 10.1093/nar/gkab382)
</li>
<li>
Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H., & Kanehisa, M. (1999). KEGG: Kyoto
Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H., & Kanehisa, M. (1999). KEGG:
Kyoto
Encyclopedia of Genes and Genomes. Nucleic acids research, 27(1), 29–34.
https://doi.org/10.1093/nar/27.1.29
</li>
<li>
Tsugawa, H., Cajka, T., Kind, T., Ma, Y., Higgins, B., Ikeda, K., Kanazawa, M., VanderGheynst,
Tsugawa, H., Cajka, T., Kind, T., Ma, Y., Higgins, B., Ikeda, K., Kanazawa, M.,
VanderGheynst,
J., Fiehn, O., & Arita, M. (2015). MS-DIAL: data-independent MS/MS deconvolution for
comprehensive metabolome analysis. Nature methods, 12(6), 523–526.
https://doi.org/10.1038/nmeth.3393
</li>
<li>
Sud M, Fahy E, Cotter D, Brown A, Dennis EA, Glass CK, Merrill AH Jr, Murphy RC, Raetz CR,
Russell DW, Subramaniam S., LMSD: LIPID MAPS® structure database Nucleic Acids Research, 35: p.
Sud M, Fahy E, Cotter D, Brown A, Dennis EA, Glass CK, Merrill AH Jr, Murphy RC, Raetz
CR,
Russell DW, Subramaniam S., LMSD: LIPID MAPS® structure database Nucleic Acids Research,
35: p.
D527-32., DOI: 10.1093/nar/gkl838 , PMID: 17098933
</li>
<li>
Fahy E, Sud M, Cotter D & Subramaniam S., LIPID MAPS® online tools for lipid research Nucleic
Fahy E, Sud M, Cotter D & Subramaniam S., LIPID MAPS® online tools for lipid research
Nucleic
Acids Research (2007), 35: p. W606-12., DOI: 10.1093/nar/gkm324 , PMID: 17584797
</li>
<li>
Wishart DS, Guo AC, Oler E, et al., HMDB 5.0: the Human Metabolome Database for 2022. Nucleic
Wishart DS, Guo AC, Oler E, et al., HMDB 5.0: the Human Metabolome Database for 2022.
Nucleic
Acids Res. 2022. Jan 7;50(D1):D622–31. 34986597
</li>
<li>
Mingxun Wang, Jeremy J. Carver, Vanessa V. Phelan, Laura M. Sanchez, Neha Garg, Yao Peng, Don
Duy Nguyen et al. "Sharing and community curation of mass spectrometry data with Global Natural
Mingxun Wang, Jeremy J. Carver, Vanessa V. Phelan, Laura M. Sanchez, Neha Garg, Yao
Peng, Don
Duy Nguyen et al. "Sharing and community curation of mass spectrometry data with Global
Natural
Products Social Molecular Networking." Nature biotechnology 34, no. 8 (2016): 828. PMID:
27504778
</li>

<li>Li, Y., Kind, T., Folz, J. et al. Spectral entropy outperforms MS/MS dot product similarity for
<li>Li, Y., Kind, T., Folz, J. et al. Spectral entropy outperforms MS/MS dot product
similarity for
small-molecule compound identification. Nat Methods 18, 1524–1531 (2021).
https://doi.org/10.1038/s41592-021-01331-z
</li>
<li>Kind, T., Fiehn, O. Seven Golden Rules for heuristic filtering of molecular formulas obtained by
<li>Kind, T., Fiehn, O. Seven Golden Rules for heuristic filtering of molecular formulas
obtained by
accurate mass spectrometry. BMC Bioinformatics 8, 105 (2007).
https://doi.org/10.1186/1471-2105-8-105
</li>
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