BioTorrents http://www.biotorrents.net/ ChemistryRelease 1.2.6 of the Chemistry Development Kit. Files: cdk-1.2.6.jar Release information is available at: http://chem-bla-ics.blogspot.com/2010/07/cdk-126-changes-and-authors.html http://www.biotorrents.net/details.php?id=95&hit=1 BioinformaticsBio-Linux 6.0 is a fully featured, powerful, configurable and easy to maintain bioinformatics workstation. Bio-Linux provides more than 500 bioinformatics programs on an Ubuntu Linux 10.04 base. There is a graphical menu for bioinformatics programs, as well as easy access to the Bio-Linux bioinformatics documentation system and sample data useful for testing programs. You can also install Bio-Linux packages to handle new generation sequence data types. Bio-Linux is built on open source systems and software, and so is free to to install and use. See http://nebc.nerc.ac.uk/tools/bio-linux/bio-linux-6.0 for more information and license description. http://www.biotorrents.net/details.php?id=90&hit=1 Papers==Brief== This contains all scientific papers published by the Public Library of Science (PLoS) journals: http://www.plos.org ==Description== The manuscripts are in PDF format and were downloaded using the PHP script, "GetPLoS.php" (included) for the following journals: PLoS Biology "http://www.plosbiology.org/" PLoS Medicine "http://www.plosmedicine.org/" PLoS Computational Biology "http://www.ploscompbiol.org/" PLoS Genetics "http://www.plosgenetics.org/" PLoS Pathogens "http://www.plospathogens.org/" PLoS Neglected Tropical Diseases "http://www.plosntds.org/" PLoS ONE "http://www.plosone.org/" ==License== All PLOS journals are "open access" under a Creative Commons license (http://www.plos.org/journals/license.php) ==Automatic Updating== This dataset will be updated monthly and can be subscribed to using the BioTorrents RSS feed: http://www.biotorrents.net/rss.php?ver=6 The downloads will placed into a folder called "all_plos_pdf". If you subscribe to the RSS feed for this torrent with your BitTorrent client you can receive automated updates for this dataset (http://www.biotorrents.net/forums.php?action=viewtopic&topicid=14 ). For example, when a new version is released your BitTorrent client will download the new torrent, check to see what is different or needs to be updated, and downloads only those new/changed files. See the Forums for further explanation:http://www.biotorrents.net/forums.php?action=viewtopic&topicid=16 ==Statistics== Total number of manuscripts: 20694 Last Updated: 2010-06-04 http://www.biotorrents.net/details.php?id=89&hit=1 GenomicsSupporting material for Darling, Mau, Perna 2010 "progressiveMauve: Multiple genome alignment with gene gain, loss, and rearrangement". This archive contains a 41-way whole genome multiple alignment of Escherichia and Shigella species computed by progressiveMauve. Some of the genomes are unfinished draft sequences. The main alignment file is called newbugs_bb and is in the XMFA alignment format. Genome data is included in GenBank flat file format where available, for some organisms it is in FastA format. http://www.biotorrents.net/details.php?id=87&hit=1 GenomicsHuman and Mouse whole genome alignment constructed using progressiveMauve from Mauve 2.3.1. The human is the hg19 goldenpath assembly from the UCSC browser, the mouse is the mm9 assembly. The alignment required about 90GB of memory and 24 hours of compute. http://www.biotorrents.net/details.php?id=86&hit=1 Chemistry*************************************************************************** * * Title: ChEMBL MySQL Torrent * * Release: chembl_04 * * Date: 01/06/2010 * * Further Info: http://www.ebi.ac.uk/chembl/ * * FTP Site: ftp://ftp.ebi.ac.uk/pub/databases/chembl/ * *************************************************************************** Description of Files in Torrent ------------------------------- chembl_04_erd_mysql.png Schema diagram chembl_04.mysqldump.sql MySQL dump file INSTALL Installation instructions http://www.biotorrents.net/details.php?id=85&hit=1 Chemistry*************************************************************************** * * Title: ChEMBL Flat File Torrent * * Release: chembl_04 * * Date: 01/06/2010 * * Further Info: http://www.ebi.ac.uk/chembl/ * * FTP Site: ftp://ftp.ebi.ac.uk/pub/databases/chembl/ * *************************************************************************** Description of Files in Torrent ------------------------------- chembl_04_release_notes.txt chembl_04 release details, which includes counts and schema change information chembl_04.fa.gz Fasta file of proteins in chembl_04 target_dictionary table chembl_04.sdf.gz SDF of chembl_04 compounds chembl_04_chemreps.txt.gz Tab-separated file containing different chemical representations (SMILES, InChI and InChI Key) of chembl_04 compounds downgraded_compounds.txt Look-up file of old and replacement molregnos http://www.biotorrents.net/details.php?id=83&hit=1 GenomicsPublication and data from "De novo Assembly of a 40 Mb Eukaryotic Genome from Short Sequence Reads: Sordaria macrospora, a Model Organism for Fungal Morphogenesis" This torrent includes: - the complete supplemental data in one place (publication_PLoSGen_2010) - the genome data and the various features extracted (annotation) Pfam and ortholog calls in the genome coordinates are provided. gbrowse directory contains data for the genome browser and .conf file that is available http://gb2.fungalgenomes.org/gb2/gbrowse/sordaria_macrospora/ - raw data used for the assembly (assembly) including the scaffolded assembly input and output to Mercator and the raw tracefiles from SRA for the accession SRA010462. The raw trace data may be suitable for additional benchmarking assemblers on a low-repeat fungal genome sized dataset. http://www.biotorrents.net/details.php?id=80&hit=1 BioinformaticsQIIME (canonically pronounced "Chime") stands for "Quantitative Insights Into Microbial Ecology". QIIME is a microbial community analysis toolkit developed in Python using PyCogent, and can be used for microbial ecology studies based on traditional and high-throughput sequencing methods. The best source of information on QIIME is the QIIME homepage: http://qiime.sourceforge.net/ http://www.biotorrents.net/details.php?id=69&hit=1 TranscriptomicsTorrent includes supplemental results and assembled transcriptomes for kiwi (Actinidia sp.) and related members of the Ericales. Full citation: Shi, T., H. Huang, and M. S. Barker. 2010. Ancient genome duplications during the evolution of kiwifruit (Actinidia) and related Ericales. Annals of Botany 106: 497-504. Full text: http://dx.doi.org/10.1093/aob/mcq129 http://www.biotorrents.net/details.php?id=68&hit=1 TranscriptomicsTorrent includes transcriptome assembly and associated files for Noug (Guizotia abyssinica) Full citation: Dempewolf, H., N. C. Kane, K. L. Ostevik, M. Geleta, M. S. Barker, Z. Lai, M. L. Stewart, E. Bekele, J. M. M. Engels, Q. C. B. Cronk, and L. H. Rieseberg. 2010. Establishing genomic tools and resources for Guizotia abyssinica (L.f.) Cass. - the development of a library of expressed sequence tags, microsatellite loci and the sequencing of its chloroplast genome. Molecular Ecology Resources in press. Full text: http://dx.doi.org/10.1111/j.1755-0998.2010.02859.x http://www.biotorrents.net/details.php?id=66&hit=1 TranscriptomicsTorrent includes supplemental results and assembled transcriptomes for 3 species of Brassicales. Full citation: Barker, M. S., H. Vogel, and M. E. Schranz. 2009. Paleopolyploidy in the Brassicales: Analyses of the Cleome transcriptome elucidate the history of genome duplications in Arabidopsis and other Brassicales. Genome Biology and Evolution 1(1): 391-399. Full text: http://dx.doi.org/10.1093/gbe/evp040 http://www.biotorrents.net/details.php?id=65&hit=1 TranscriptomicsAssembled unigenes used to develop Helianthus and Helianthus annuus microarrays by members of the Rieseberg and Knapp labs in collaboration with other researchers at the Compositae Genome Project (http://compgenomics.ucdavis.edu/) and HeliaGene (http://www.heliagene.org/) Assemblies were constructed with Helianthus EST sequences available on Genbank 9 Sep 2007 and additional ESTs from Steve Knapp's lab. The assembly pipeline starts with Seqclean to remove poor quality sequences, clip poor quality ends, and trim vector. Prior to contiging, a library-less repeat masker, RBR, was used to dynamically identify and mask repeats with the default settings. Contigs were constructed using TGICL with default settings, and a final file called *.unigenes containing contigs and singletons was constructed. A total of 33,376 unigenes were assembled from a starting pool of 94,706 ESTs for Helianthus annuus. A total of 87,237 unigenes were assembled from a starting pool of 284,340 ESTs for all species of Helianthus. All files produced during this assembly are available in each assembly archive. Manuscript forthcoming - contact Mike Barker for more information (msbarker@biodiversity.ubc.ca) http://www.biotorrents.net/details.php?id=64&hit=1 TranscriptomicsTorrent includes supplemental results and assembled transcriptomes for 18 species of Compositae. Full citation: Barker, M. S., N. C. Kane, M. Matvienko, A. Kozik, R. W. Michelmore, S. J. Knapp, and L. H. Rieseberg. 2008. Multiple paleopolyploidizations during the evolution of the Compositae reveal parallel patterns of duplicate gene retention after millions of years. Molecular Biology and Evolution 25(11): 2445-2455. Full text: http://dx.doi.org/10.1093/molbev/msn187 http://www.biotorrents.net/details.php?id=63&hit=1 BioinformaticsQIIME (canonically pronounced "Chime") stands for "Quantitative Insights Into Microbial Ecology". QIIME is a microbial community analysis toolkit developed in Python using PyCogent, and can be used for microbial ecology studies based on traditional and high-throughput sequencing methods. The best source of information on QIIME is the QIIME homepage: http://qiime.sourceforge.net/ http://www.biotorrents.net/details.php?id=62&hit=1