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stuppie / create_compil

Pipeline for creating compil database for gut microbiome metaproteomics
MIT License
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Add new data sources #1

Open stuppie opened 7 years ago

stuppie commented 7 years ago

Done:

Food https://docs.google.com/spreadsheets/d/11TXjYjJelW26wPHQw6Fzl7rtHc-LzCuDihbzfktuC78/edit?usp=sharing

peptide standard peptide sequences https://www.lifetechnologies.com/order/catalog/product/88320

P00000 Pierce Peptide Retention Time Calibration Mixture SSAAPPPPPRGISNEGQNASIKHVLTSIGEKDIPVPKPKIGDYAGIKTASEFDSAIAQDKSAAGAFGPELSRELGQSGVDTYLQTKGLILVGGYGTR GILFVGSGVSGGEEGARSFANQPLEVVYSKLTILEELRNGFILDGFPRELASGLSFPVGFKLSSEAPALFQFDLK

A Catalogue of the Mouse Gut Metagenome http://gigadb.org/dataset/view/id/100114/token/mZlMYJIF04LshpgP http://www.nature.com/nbt/journal/v33/n10/full/nbt.3353.html Xiao, L., et al., A catalog of the mouse gut metagenome. Nat Biotech, 2015. 33(10): p. 1103-1108.

stuppie commented 7 years ago

TODO integrated gene catalog (IGC) http://www.nature.com/nbt/journal/v32/n8/full/nbt.2942.html http://meta.genomics.cn/meta/dataTools

ORNL - Jansson Study 2007 http://www.nature.com/ismej/journal/v3/n2/full/ismej2008108a.html#tbl1 http://compbio.ornl.gov/human_gut_microbial_metaproteome/databases/

Mouse Intestinal Bacterial Collection (miBC) http://www.nature.com/articles/nmicrobiol2016131 https://www.dsmz.de/catalogues/dzif-sammlung-der-dsmz/maus-mikrobiomliste.html https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJEB10572 Lagkouvardos, I., et al., Nature Microbiology, 2016. 1: p. 16131. Can't find assembled data?

stuppie commented 7 years ago 
https://github.com/galaxyproteomics/tools-galaxyp/issues/87