Mercurial > repos > pieterlukasse > prims_metabolomics
annotate README.rst @ 21:19d8fd10248e
* Added interface to METEXP data store, including tool to fire queries in batch mode
* Improved quantification output files of MsClust, a.o. sorting
mass list based on intensity (last two columns of quantification
files)
* Added Molecular Mass calculation method
| author | pieter.lukasse@wur.nl |
|---|---|
| date | Wed, 05 Mar 2014 17:20:11 +0100 |
| parents | a35b55bfe96c |
| children | 385d21a8d0a0 |
| rev | line source |
|---|---|
| 0 | 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 | |
| 1 | 6 Retention Index (RI) based Quality Control (RIQC) for Mass Spectrometry metabolomics data. |
| 0 | 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), | |
| 2 | 11 Wageningen, The Netherlands. All rights reserved. See the license text below. |
| 0 | 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 -------------- ---------------------------------------------------------------------- | |
|
21
19d8fd10248e
* Added interface to METEXP data store, including tool to fire queries in batch mode
pieter.lukasse@wur.nl
parents:
2
diff
changeset
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22 March 2014 * Added interface to METEXP data store, including tool to fire |
|
19d8fd10248e
* Added interface to METEXP data store, including tool to fire queries in batch mode
pieter.lukasse@wur.nl
parents:
2
diff
changeset
|
23 queries in batch mode |
|
19d8fd10248e
* Added interface to METEXP data store, including tool to fire queries in batch mode
pieter.lukasse@wur.nl
parents:
2
diff
changeset
|
24 * Improved quantification output files of MsClust, a.o. sorting |
|
19d8fd10248e
* Added interface to METEXP data store, including tool to fire queries in batch mode
pieter.lukasse@wur.nl
parents:
2
diff
changeset
|
25 mass list based on intensity (last two columns of quantification |
|
19d8fd10248e
* Added interface to METEXP data store, including tool to fire queries in batch mode
pieter.lukasse@wur.nl
parents:
2
diff
changeset
|
26 files) |
| 0 | 27 January 2014 * first release via Tool Shed, combining the RIQC and MsClust in a |
| 28 single package (this package) | |
| 29 * integration with METEXP software (data store for metabolomics | |
| 30 experiments with respective metadata and identifications) | |
| 31 2013 * hand-over of the NIST_UTIL and RIQC tools from the NBIC team to | |
| 32 Plant Research International | |
| 33 2012 * development of MsClust 2.0, making it also suitable for Galaxy | |
| 34 <2011 * development and publication of MsClust 1.0 | |
| 35 ============== ====================================================================== | |
| 36 | |
| 37 Tool Versioning | |
| 38 =============== | |
| 39 | |
| 40 PRIMS tools will have versions of the form X.Y.Z. Versions | |
| 41 differing only after the second decimal should be completely | |
| 42 compatible with each other. Breaking changes should result in an | |
| 43 increment of the number before and/or after the first decimal. All | |
| 44 tools of version less than 1.0.0 should be considered beta. | |
| 45 | |
| 46 | |
| 47 Bug Reports & other questions | |
| 48 ============================= | |
| 49 | |
| 50 For the time being issues can be reported via the contact form at: | |
| 51 http://www.wageningenur.nl/en/Persons/PNJ-Pieter-Lukasse.htm | |
| 52 | |
| 53 Developers, Contributions & Collaborations | |
| 54 ========================================== | |
| 55 | |
| 56 If you wish to join forces and collaborate on some of the | |
| 57 tools do not hesitate to contact Pieter Lukasse via the contact form above. | |
| 58 | |
| 59 | |
| 60 License (Apache, Version 2.0) | |
| 61 ============================= | |
| 62 | |
| 63 Copyright 2013 Pieter Lukasse, Plant Research International (PRI). | |
| 64 | |
| 65 Licensed under the Apache License, Version 2.0 (the "License"); | |
| 66 you may not use this software except in compliance with the License. | |
| 67 You may obtain a copy of the License at | |
| 68 | |
| 69 http://www.apache.org/licenses/LICENSE-2.0 | |
| 70 | |
| 71 Unless required by applicable law or agreed to in writing, software | |
| 72 distributed under the License is distributed on an "AS IS" BASIS, | |
| 73 WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | |
| 74 See the License for the specific language governing permissions and | |
| 75 limitations under the License. | |
| 76 |