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