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METAREP DIRECTORIES /app web application files /cake cake framework files /data example datasets /scripts perl and R scripts /doc documentation /db relational databases /solr solr/lucene configuration files /vendors 3rd-party php tools INSTALLATION AND ADDTIONAL INFORMATION Please visit the project's wiki page at http://wiki.github.com/jcvi/METAREP for additional information. The 1.3.2 installation guide can be found at https://github.com/jcvi/METAREP/wiki/Installation-Guide-v-1.3.2 VIDEO DOCUMENTATION 5 min overview http://www.youtube.com/watch?v=DJNjM7LMVWU web tutorial http://www.youtube.com/watch?v=7FPJaPyLjMk&feature=relmfu implementation details http://www.youtube.com/watch?v=j0rlTIkvfvI RELEASE NOTES JCVI Metagenomics Reports - Version 1.4.0 New Feature: METAREP-461 Import dataset option for Admin via project page METAREP-206 New Blast Page to find homologous sequences in selected datasets, display and export results METAREP-460 New Search Page option to search datasets using user defined sequences at three homology cut-off levels (1E-5, 1E-20 and 1E-50) METAREP-461 Deprecate common name field in Compare Page (will be replaced with a high level summary, similar to the View Page Summary tab in the next release) METAREP-462 Adjust Compare Page Layout for new versions of Chrome/Firefox METAREP-435 New project link shortcut from user dashboard page project listings METAREP-434 Select datasets for population creation by filtering datasets based on descriptions METAREP-437 Updated download file header METAREP-421 Fisher's Exact Test to compare two datasets (exact test) METAREP-422 Equality of Proportions Test to compare two datasets (large sample approximation) METAREP-432 False Discovery Rate calculation and filtering for multiple testing correction METAREP-424 Compare two pathway maps with log odds ratio and significance color coding (available for 'Statistical tests (2 datasets)' option on the KEGG pathway level; click on image in the last column) JCVI Metagenomics Reports - Version 1.3.2 (bug fix release) Bug Fixes: METAREP-477 Mosaic Plot option was missing in scripts/r/plots.r METAREP-478 Population creation process expected core organization by project ID; the process was fixed to work with a root level core organization as generated by the metarep_loader.pl script. -- JCVI Metagenomics Reports - Version 1.3.1 New Feature: METAREP-391 update viral evidence summary for view page METAREP-409 update NCBI taxonomy, KEGG, GO, and enzymes: NCBI taxonomy version 09/30/2011: 280,602 new taxa KEGG version 09/01/2011: 21 new KEGG KO pathways; 1 new KEGG EC pathway Gene Ontology version 09/05/2011 METAREP-407 implement GO slim support for compare page METAREP-406 implement mosaic plot option for compare page METAREP-205 sequence export option for search page Bug Fixes: METAREP-408 fix compare panel misalignment -- JCVI Metagenomics Reports - Version 1.2.0 Improvement METAREP-244 - Increased speed of web page build-up METAREP-247 - Integrate new METAREP logo into web layout New Feature METAREP-228 - Added unresolved taxonomy fractions to Browse APIS pages METAREP-243 - Search datasets using name based searches for Taxonomy, HMM, Enzymes, GO and KEGG pathway names METAREP-245 - Added search option to filter Browse Taxonomy/GO/Pathway/EC pages METAREP-248 - Implemented PHP based load balancing option Bug Fixes METAREP-246 - Fix View Download Cache Issue -- JCVI Metagenomics Reports - Version 1.1.0 New Feature METAREP-215 - Search all datasets option; generate meta-information summaries METAREP-217 - Allow users to test METAREP without creating an account METAREP-218 - Allow distance matrix export for hierarchical clustering, heatmap, mds plots METAREP-219 - Added color legend to heatmap METAREP-220 - Fixed search example links in search help dialog METAREP-221 - Use new radio buttons in compare page to limit selection to project datasets METAREP-223 - Compare datasets using Wilcoxon Rank Sum Test METAREP-224 - Ajax support for search dataset pages --