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1 PRIMS-metabolomics toolset & Galaxy wrappers
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2 ============================================
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3
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4 Metabolomics module of Plant Research International's Mass Spectrometry (PRIMS) toolsuite.
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5 This toolset consists of custom tools to enable metabolite identifications and
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6 Retention Index (RI) based Quality Control (RIQC) for Mass Spectrometry metabolomics data.
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7
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8 Copyright:
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9 * 2012: NIST_UTIL and RIQC tools: Copyright (c) 2012 Maarten Kooyman and Marcel Kempenaar, NBIC BRS
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10 * 2013: all tools: Copyright (c) 2013 by Pieter Lukasse, Plant Research International (PRI),
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11 Wageningen, The Netherlands. All rights reserved. See the license text below.
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12
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13 Galaxy wrappers and installation are available from the Galaxy Tool Shed at:
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14 http://toolshed.g2.bx.psu.edu/view/pieterlukasse/prims_metabolomics
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15
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16 History
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17 =======
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18
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19 ============== ======================================================================
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20 Date Changes
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21 -------------- ----------------------------------------------------------------------
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22 December 2014 * Added MsClust support for parsing XCMS alignment results.
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23 * Improved output reports for XCMS wrappers.
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24 November 2014 * Added XCMS related tool wrappers (for metaMS and diffreport)
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25 September 2014 * Added new membership cutoff option for final clusters in MsClust
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26 * Improved MsClust memory usage for large datasets
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27 * Simplified MsClust HTML report
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28 * Added option for microminutes based clustering instead of scannr
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29 based in MsClust
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30 April 2014 * Added interface to ExactMassDB, Pep1000, KEGG, KNApSAcK, Flavonoid
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31 Viewer, LipidMAPS, HMDB, PubChem, by using the service MFSearcher.
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32 This enables users to query multiple public repositories for
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33 elemental compositions from accurate mass values detected by
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34 high-resolution mass spectrometers. NB: see also added
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35 licensing info below.
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36 March 2014 * Added interface to METEXP data store, including tool to fire
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37 queries in batch mode
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38 * Improved quantification output files of MsClust, a.o. sorting
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39 mass list based on intensity (last two columns of quantification
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40 files)
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41 January 2014 * first release via Tool Shed, combining the RIQC and MsClust in a
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42 single package (this package)
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43 * integration with METEXP software (data store for metabolomics
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44 experiments with respective metadata and identifications)
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45 2013 * hand-over of the NIST_UTIL and RIQC tools from the NBIC team to
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46 Plant Research International
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47 2012 * development of MsClust 2.0, making it also suitable for Galaxy
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48 <2011 * development and publication of MsClust 1.0
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49 ============== ======================================================================
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50
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51 Tool Versioning
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52 ===============
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53
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54 PRIMS tools will have versions of the form X.Y.Z. Versions
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55 differing only after the second decimal should be completely
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56 compatible with each other. Breaking changes should result in an
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57 increment of the number before and/or after the first decimal. All
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58 tools of version less than 1.0.0 should be considered beta.
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59
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60
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61 Bug Reports & other questions
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62 =============================
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63
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64 For the time being issues can be reported via the contact form at:
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65 http://www.wageningenur.nl/en/Persons/PNJ-Pieter-Lukasse.htm
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66
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67 Developers, Contributions & Collaborations
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68 ==========================================
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69
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70 If you wish to join forces and collaborate on some of the
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71 tools do not hesitate to contact Pieter Lukasse via the contact form above.
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72
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73
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74 License (Apache, Version 2.0)
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75 =============================
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76
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77 Copyright 2013 Pieter Lukasse, Plant Research International (PRI).
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78
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79 Licensed under the Apache License, Version 2.0 (the "License");
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80 you may not use this software except in compliance with the License.
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81 You may obtain a copy of the License at
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82
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83 http://www.apache.org/licenses/LICENSE-2.0
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84
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85 Unless required by applicable law or agreed to in writing, software
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86 distributed under the License is distributed on an "AS IS" BASIS,
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87 WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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88 See the License for the specific language governing permissions and
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89 limitations under the License.
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90
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91
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92 License for third party services
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93 ================================
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94 MFSearcher service : http://webs2.kazusa.or.jp/mfsearcher/#090
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95 In the MFSearcher system, the compound data provided by KEGG, Flavonoid Viewer, LIPID MAPS, HMDB and PubChem
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96 were downloaded for academic purposes. The compound data of KNApSAcK is provided by Prof. Kanaya in
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97 Nara Institute of Science and Technology (NAIST). The part of these data are utilized to construct the
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98 specified databases for rapid mass searching in the MFSearcher system after re-calculating the molecular weights.
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99 Please preserve the contracts of each original databases when utilizing the search results against these
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100 databases by MFSearcher.
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101
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102 The searching system of MFSearcher, the ExactMassDB database, and the Pep1000 database by Kazusa DNA
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103 Research Institute is licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported License. |
