From 7912f6eae2ad2da1552534b60963d2062c698a6e Mon Sep 17 00:00:00 2001 From: Jamie Collins Date: Mon, 30 Aug 2021 12:32:20 -0700 Subject: [PATCH] Updating authors and creators to account for personnel changes; updated dates in copyright; some versioning updates as well --- DESCRIPTION | 19 +++++++++++-------- LICENSE | 8 ++++---- README.md | 6 +++--- inst/CITATION | 2 +- inst/NEWS | 8 ++++++-- 5 files changed, 25 insertions(+), 18 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index a98bed5..484a663 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,18 +1,18 @@ Package: LOBSTAHS Title: Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences -Version: 1.19.0 -Date: 2018-04-13 +Version: 1.19.1 +Date: 2021-08-30 Authors@R: c( person("James", "Collins", email = "james.r.collins@aya.yale.edu", role = c("aut", "cre")), person("Helen", "Fredricks", email = "hfredricks@whoi.edu", role = c("aut")), person("Bethanie", "Edwards", email = "bedwards@whoi.edu", role = c("aut")), - person("Benjamin", "Van Mooy", email = "bvanmooy@whoi.edu", role = c("aut")), - person("Tyrone", "Lee", email = "tlee@whoi.edu", + person("Benjamin", "Van Mooy", email = "bvanmooy@whoi.edu", role = c("aut")), - person("Henry", "Holm", email = "hholm@whoi.edu", - role = c("aut")) + person("Daniel", "Lowenstein", email = "dlowenstein@whoi.edu", + role = c("aut")), + person("Henry", "Holm", email = "hholm@whoi.edu", role = c("aut")) ) Depends: R (>= 3.4), @@ -46,5 +46,8 @@ VignetteBuilder: knitr biocViews: ImmunoOncology, MassSpectrometry, Metabolomics, Lipidomics, DataImport NeedsCompilation: no Author: James Collins [aut, cre], Helen Fredricks [aut], Bethanie - Edwards [aut], Tyrone Lee [aut], Henry Holm [aut] Benjamin Van Mooy [aut] -Maintainer: James Collins , Tyrone Lee , Henry Holm + Edwards [aut], Tyrone Lee [aut], Henry Holm [aut], + Benjamin Van Mooy [aut], Daniel Lowenstein [aut] +Maintainer: James Collins , + Henry Holm , + Daniel Lowenstein \ No newline at end of file diff --git a/LICENSE b/LICENSE index b4eed92..3981c5d 100755 --- a/LICENSE +++ b/LICENSE @@ -3,10 +3,10 @@ putative identification of mass spectral features in large, HPLC-MS lipid datasets, including custom onboard containing data for lipids and oxidized lipids. -All code copyright (c) 2015-2017, the following members of the Van Mooy -Laboratory group at Woods Hole Oceanographic Institution: James R. Collins, -Bethanie R. Edwards, Helen F. Fredricks, and Benjamin A.S. Van Mooy. All -accompanying written materials copyright (c) 2015-2017, James R. Collins. +All code and accompanying written materials copyright (c) 2015-2021, the +following current and former members of the Van Mooy Laboratory group at Woods +Hole Oceanographic Institution: James R. Collins, Bethanie R. Edwards, Helen +F. Fredricks, Henry C. Holm, Daniel Lowenstein, and Benjamin A.S. Van Mooy. This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free diff --git a/README.md b/README.md index a7a1e5b..e40d0a8 100755 --- a/README.md +++ b/README.md @@ -6,7 +6,7 @@ The primary repository at [https://github.com/vanmooylipidomics/LOBSTAHS](https: A [comprehensive vignette](https://github.com/vanmooylipidomics/LOBSTAHS/blob/master/vignettes/LOBSTAHS.Rmd) contains detailed, step-by-step user instructions and examples of package functions illustrated with a model dataset. -LOBSTAHS is copyright (c) 2015-2017, by the following current and former members of the Van Mooy Laboratory group at Woods Hole Oceanographic Institution: [James R. Collins](http://jamesrco.github.io), Bethanie R. Edwards, Helen F. Fredricks, and Benjamin A.S. Van Mooy. All accompanying written materials are copyright (c) 2015-2017, James R. Collins. LOBSTAHS is provided under the [GNU General Public License](https://github.com/vanmooylipidomics/LOBSTAHS/blob/master/LICENSE) and subject to terms of reuse as specified therein. +LOBSTAHS and all accompanying written materials are copyright (c) 2015-2021, by the following current and former members of the Van Mooy Laboratory group at Woods Hole Oceanographic Institution: [James R. Collins](http://jamesrco.github.io), Bethanie R. Edwards, Daniel Lowenstein, Henry Holm, Helen F. Fredricks, and Benjamin A.S. Van Mooy. LOBSTAHS is provided under the [GNU General Public License](https://github.com/vanmooylipidomics/LOBSTAHS/blob/master/LICENSE) and subject to terms of reuse as specified therein.

Citations

@@ -108,7 +108,7 @@ HPLC-MS data must be assembled into a CAMERA xsAnnotate object prior to analysis * total acyl carbon chain length, and * degree of acyl carbon chain unsaturation (i.e., number of double bonds) -Alternatively, users may load the LOBSTAHS default databases. These contain entries for a wide range of intact polar diacylglycerols (IP-DAG), triacylglycerols (TAG), polyunsaturated aldehydes (PUAs), free fatty acids (FFA), and common photosynthetic pigments. In addition, the latest LOBSTAHS release includes support for lyso lipids under an "IP_MAG" species class and certain glycosphingolipids, ceramides, betaine-like lipids (BLL), bile salts, wax esters, cholesterols, mass spectral contaminants, and quinones. Functionality for other lipid classes is added regularly. The default databases (as of November 8, 2017) include 25,741 and 21,063 unique compounds that can be identifed in positive and negative ionization mode data, respectively. +Alternatively, users may load the LOBSTAHS default databases. These contain entries for a wide range of intact polar diacylglycerols (IP-DAG), triacylglycerols (TAG), polyunsaturated aldehydes (PUAs), free fatty acids (FFA), and common photosynthetic pigments. In addition, the latest LOBSTAHS release includes support for lyso lipids under an "IP_MAG" species class and certain glycosphingolipids, ceramides, betaine-like lipids (BLL), bile salts, wax esters, cholesterols, mass spectral contaminants, and quinones. Functionality for other lipid classes is added regularly. The default databases (as of August 30, 2021) include 25,741 and 21,063 unique compounds that can be identifed in positive and negative ionization mode data, respectively.

Identification, screening, and annotation using orthogonal criteria

@@ -128,4 +128,4 @@ The package [**PtH2O2lipids**](https://github.com/vanmooylipidomics/PtH2O2lipids Scripts used to generate the figures and many of the tables in the above referenced manuscript can be found at https://github.com/jamesrco/LipidomicsDataViz/tree/master/LOBSTAHS -LOBSTAHS is maintained by [Jamie Collins](https://jamesrco.github.io) and collaborators in the [Van Mooy Lab](https://github.com/vanmooylipidomics) at WHOI. +LOBSTAHS is maintained by [Jamie Collins](https://jamesrco.github.io), [Henry Holm](https://hholm.github.io), Daniel Lowenstein and other collaborators in the [Van Mooy Lab](https://github.com/vanmooylipidomics) at WHOI. diff --git a/inst/CITATION b/inst/CITATION index 3e34486..bd3487f 100644 --- a/inst/CITATION +++ b/inst/CITATION @@ -30,6 +30,6 @@ citEntry(entry="misc", "B. A. S. Van Mooy. 2017.", "LOBSTAHS: An adduct-based lipidomics strategy for", "discovery and identification of oxidative stress", - "biomarkers. R package version 1.5.0;", + "biomarkers. R package version 1.19.1;", "doi:10.18129/B9.bioc.LOBSTAHS")) diff --git a/inst/NEWS b/inst/NEWS index 59979ba..1a095de 100644 --- a/inst/NEWS +++ b/inst/NEWS @@ -1,5 +1,9 @@ 1.0.0 (2016-04-21) jrcollins * Initial release for Bioconductor 1.5.1 (2017-04-11) jrcollins - * added trimmed_database - * added doLOBscreen check for physically unlikely oxidated molecules \ No newline at end of file + * Added trimmed_database + * Added doLOBscreen check for physically unlikely oxidated molecules +1.19.1 (2021-08-30) jrcollins + * Updated authors and maintainers + * Formalized support for new lipid classes including bile salts, wax esters, + quinones, etc. \ No newline at end of file