TODO

• JSON format description
• Modify normalization from None to Broad DSGC DONE
• include whole datasets export URLs in Export tab DONE
• setup gimm14 DONE
• logo at landing page DONE
• Workflow description
• User's tutorial DONE
• Developers' tutorial DONE
• Start from existing MySQL database DONE
• Homepage link under piLINCS logo DONE
• Debug quantile normalization DONE
• Implement and test z-score normalization
• Assay name (P100, GCP, L1000 etc.) should be added to quick search; DONE
• Full n-tuple description (cell, perturbation, dose, time etc.) for each profile should be available in 'profile' DONE
• Full n-tuple description (cell, perturbation, dose, time etc.) for each profile should be available 'merged profile' view (how exactly is another matter, we do not want this to be too clunky);
• Names of profiles in 'merged profile' view should be links to raw data with rows corresponding to replicates that were used for aggregation/merging;
• One possibility is that we simply cross-link RunID back to raw data;
• When exporting JSON file with merged profiles, the exported files should be self-sufficient, i.e., columns/rows (properly added to JSON hierarchical structure) with peptide and experiment (n-tuple) description should be included;
• In addition to JSON, a simple csv (or other text format consistent with Excel) export format needs to be added, containing rows with merged profiles and columns with peptides/probes for P100, GCP and other assays in the future.
• In 'merged profile' view individual bars representing peptide abundance should be labeled (when hovering mouse);
• Re-normalized data should be made available in 'profile' and 'merged profile' views, just like the original data;
• Visualization of P100/GCP data sets provided by Avi's group (including their 'clustergrams') should be cross-linked (or perhaps added directly as another tab instead of our previous heatmap tab); DONE
• Little bugs: export button in Firefox (and other browser issues), negative page numbers when displaying less than a few pages of data in merged profiles. DONE
• Add search terms to URL (analyze in ilincs) DONE