grnsight 6.0.4 → 7.1.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (1245) hide show
  1. package/.eslintrc.yml +4 -4
  2. package/database/README.md +224 -79
  3. package/database/constants.py +42 -0
  4. package/database/expression-database/README.md +2 -2
  5. package/database/expression-database/schema.sql +14 -14
  6. package/database/expression-database/scripts/loader.py +6 -6
  7. package/database/filter_update.py +168 -0
  8. package/database/grnsettings-database/README.md +52 -0
  9. package/database/grnsettings-database/schema.sql +4 -0
  10. package/database/loader.py +30 -0
  11. package/database/loader_update.py +36 -0
  12. package/database/network-database/README.md +36 -4
  13. package/database/network-database/schema.sql +7 -7
  14. package/database/network-database/scripts/generate_network.py +16 -24
  15. package/database/network-database/scripts/generate_new_network_version.py +216 -0
  16. package/database/protein-protein-database/README.md +71 -0
  17. package/database/protein-protein-database/schema.sql +37 -0
  18. package/database/protein-protein-database/scripts/generate_protein_network.py +227 -0
  19. package/database/protein-protein-database/scripts/remove_duplicates.sh +4 -0
  20. package/database/utils.py +418 -0
  21. package/package.json +2 -2
  22. package/server/app.js +2 -0
  23. package/server/config/config.js +4 -4
  24. package/server/controllers/additional-sheet-parser.js +2 -1
  25. package/server/controllers/constants.js +5 -0
  26. package/server/controllers/custom-workbook-controller.js +8 -6
  27. package/server/controllers/demo-workbooks.js +1460 -4
  28. package/server/controllers/export-constants.js +3 -2
  29. package/server/controllers/exporters/sif.js +6 -1
  30. package/server/controllers/exporters/xlsx.js +8 -3
  31. package/server/controllers/expression-sheet-parser.js +0 -6
  32. package/server/controllers/grnsettings-database-controller.js +17 -0
  33. package/server/controllers/importers/sif.js +29 -11
  34. package/server/controllers/network-database-controller.js +2 -2
  35. package/server/controllers/network-sheet-parser.js +54 -12
  36. package/server/controllers/protein-database-controller.js +18 -0
  37. package/server/controllers/sif-constants.js +4 -4
  38. package/server/controllers/spreadsheet-controller.js +44 -1
  39. package/server/controllers/workbook-constants.js +21 -4
  40. package/server/dals/expression-dal.js +8 -7
  41. package/server/dals/grnsetting-dal.js +49 -0
  42. package/server/dals/network-dal.js +13 -12
  43. package/server/dals/protein-dal.js +106 -0
  44. package/test/export-tests.js +136 -9
  45. package/test/import-sif-tests.js +54 -13
  46. package/test/test.js +1 -1
  47. package/test-files/additional-sheet-test-files/optimization-parameters-default.xlsx +0 -0
  48. package/test-files/demo-files/18_proteins_81_edges_PPI.xlsx +0 -0
  49. package/test-files/expression-data-test-sheets/expression_sheet_missing_data_ok_export_exact.xlsx +0 -0
  50. package/web-client/config/config.js +4 -4
  51. package/web-client/public/js/api/grnsight-api.js +72 -56
  52. package/web-client/public/js/constants.js +26 -12
  53. package/web-client/public/js/generateNetwork.js +173 -67
  54. package/web-client/public/js/graph.js +420 -150
  55. package/web-client/public/js/grnsight.js +25 -4
  56. package/web-client/public/js/grnstate.js +3 -1
  57. package/web-client/public/js/iframe-coordination.js +3 -3
  58. package/web-client/public/js/setup-handlers.js +28 -32
  59. package/web-client/public/js/setup-load-and-import-handlers.js +196 -170
  60. package/web-client/public/js/update-app.js +84 -17
  61. package/web-client/public/js/upload.js +193 -157
  62. package/web-client/public/lib/bootstrap.file-input/bootstrap.file-input.js +0 -1
  63. package/web-client/public/stylesheets/grnsight.styl +40 -16
  64. package/web-client/views/components/demo.pug +7 -5
  65. package/web-client/views/upload.pug +63 -49
  66. package/.bundle/config +0 -3
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  68. package/Gemfile.lock +0 -259
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- <p id="subtextLMU">A Joint Project of the<br /> LMU Bioinformatics and Biomathematics Groups</p>
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- <p id="title"><a href="/GRNsight">GRNsight</a></p>
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- <p id="subtext">Web app and service for visualizing models of gene regulatory networks.</p>
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- <p class="newsInfo">Anindita Varshneya and Mihir Samdarshi presented a poster about GRNsight at the Experimental Biology conference in San Diego. <a href="http://www.fasebj.org/content/30/1_Supplement/819.10.abstract?sid=78e46198-a079-4985-9ebd-0e286b8dde38">Abstract</a> and <a href="//www.slideshare.net/GRNsight/varshneya-samdarshi-lmusymposium2016">poster</a> by Anindita Varshneya and Mihir Samdarshi entitled, "Test-driven development improves GRNsight: a web application for visualizing models of gene regulatory networks".</p>
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- <p class="newsInfo">Anindita Varshneya and Mihir Samdarshi presented a poster about GRNsight at the 8<sup>th</sup> Annual Loyola Marymount University Undergraduate Research Conference. <a href="http://academics.lmu.edu/media/lmuacademics/undergraduateresearchsymposium/documents/ei8ht_Symposium_Long_Program_16_Secured.pdf">Abstract</a> and <a href="//www.slideshare.net/GRNsight/varshneya-samdarshi-lmusymposium2016">poster</a> by Anindita Varshneya and Mihir Samdarshi entitled, "Test-driven development improves GRNsight: a web application for visualizing models of gene regulatory networks".</p>
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- <p class="newsDate">September 29, 2015</p>
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- <p class="newsHeader">Article describing the sigmoidal dynamical model and penalized least squares approach used by our companion project, <a href="http://kdahlquist.github.io/GRNmap/publications.html">GRNmap</a>, is published online in the <i>Bulletin of Mathematical Biology</i> </p>
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- <p class="newsInfo">Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., and Wanner, N.C. (2015) Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. <i>Bulletin of Mathematical Biology</i>, 77(8), 1457-1492, published online September 29, 2015. DOI: 10.1007/s11538-015-0092-6.</p>
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- <li><a href="http://www.ncbi.nlm.nih.gov/pubmed/26420504">PubMed Abstract</a></li>
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- <li><a href="http://link.springer.com/article/10.1007/s11538-015-0092-6/fulltext.html">View full text in HTML</a></li>
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- <li><a href="http://link.springer.com/content/pdf/10.1007%2Fs11538-015-0092-6.pdf">Download PDF (1205 KB)</a></li>
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- <li><a href="http://link.springer.com/content/esm/art:10.1007/s11538-015-0092-6/file/MediaObjects/11538_2015_92_MOESM1_ESM.zip">Download electronic supplementary material (65 KB)</a></li>
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- <p class="newsDate">August 10, 2015</p>
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- <p class="newsHeader">GRNsight Reaches 1,000 Uploads</p>
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- <p class="newsInfo">GRNsight reached a total of 1,000 file uploads on the website today.</p>
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- <p class="newsDate">June 24, 2015</p>
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- <p class="newsHeader">GRNsight v1.12 Released</p>
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- <p class="newsInfo">For a description of the new features, please see the <a href="/GRNsight/about.html#v1_12Content">About page</a>.</p>
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- <p class="newsHeader">GRNsight v1.10.4 Released</p>
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- <p class="newsInfo">For a description of the new features, please see the <a href="/GRNsight/about.html#v1_10_4Content">About page</a>.</p>
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- <p class="newsHeader">West Coast Biological Sciences Undergraduate Research Conference</p>
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- <p class="newsInfo">Nicole Anguiano and Anu Varshneya presented a poster about GRNsight at the 40<sup>th</sup> Annual West Coast Biological Sciences Undergraduate Research Conference. <a href="http://www.slideshare.net/GRNsight/anguiano-varshneya-lmusymposium2015">Poster</a> by Nicole Anguiano and Anindita Varshneya entitled, "Improvements to GRNsight: a Web Application for Visualizing Models of Gene Regulatory Networks".</p>
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- The joint LMU Bioinformatics and Biomathematics groups presented posters about GRNsight and GRNmap at the 7th Annual Loyola Marymount University Undergraduate Research Symposium on March 21, 2014.
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- <li><a href="http://academics.lmu.edu/media/lmuacademics/undergraduateresearchsymposium/documents/Final%20Program%20w.%20Abstracts.pdf">Full symposium program</a></li>
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- <li><a href="http://www.slideshare.net/GRNsight/anguiano-varshneya-lmusymposium2015">Poster</a> by Nicole Anguiano and Anindita Varshneya entitled, "Improvements to GRNsight: a Web Application for Visualizing Models of Gene Regulatory Networks"</li>
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- <li><a href="images/Carrillo_Roque_LMU_Symposium_2015.pptx">Poster</a> by Juan Carrillo and Trixie Roque entitled, "Software Refactoring and Usability Enhancement for GRNmap, a Gene Regulatory Network Modeling Application"</li>
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- <li><a href="images/Johnson_Williams_LMU_Symposium_2015.pptx">Poster</a> by Natalie Williams and K. Grace Johnson entitled, "Comparing the Dynamics of the Cold Shock Gene Regulatory Network in Yeast with a Random Network"</li>
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- <p class="newsHeader">GRNsight v1.10 Released</p>
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- <p class="newsInfo">For a description of the new features, please see the <a href="/GRNsight/about.html#v1_10Content">About page</a>.</p>
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- <p class="newsHeader">GRNsight v1.8.2 Released</p>
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- <p class="newsInfo">For a description of the new features, please see the <a href="/GRNsight/about.html#v1_8_2Content">About page</a>.</p>
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- <p class="newsHeader">Southern California Systems Biology Conference</p>
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- <p class="newsInfo">Dr. Kam D. Dahlquist gives a presentation about GRNsight and GRNmap, and Nicole Anguiano gives a poster presentation about GRNsight at the <a href="http://ccbs.uci.edu/scsb2015home">5<sup>th</sup> Annual Southern California Systems Biology Conference</a>. Click <a href="http://www.slideshare.net/GRNsight/dahlquist-so-calsysbio20140131">here</a> to view the slides and <a href="http://www.slideshare.net/GRNsight/anguiano-varshneya-sccurposter20141122">here</a> to view the poster.</p>
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- <p class="newsInfo">For a description of the new features, please see the <a href="/GRNsight/about.html#v1_8Content">About page</a>.</p>
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- <p class="newsInfo">Nicole Anguiano and Anindita Varshneya give a poster presentation about GRNsight at the Southern California Conference for Undergraduate Research. Click <a href="http://www.slideshare.net/GRNsight/anguiano-varshneya-sccurposter20141122" target="_blank">here</a> to view the poster.</p>
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- <p class="newsInfo">For a description of the new features, please see the <a href="/GRNsight/about.html#v1_6Content">About page</a>.</p>
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- <p class="newsHeader">GRNsight v1.4 Released</p>
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- <p class="newsInfo">For a description of the new features, please see the <a href="/GRNsight/about.html#v1_4Content">About page</a>.</p>
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- <p class="newsHeader">GRNSight v1.2 Released</p>
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- <p class="newsInfo">For a description of the new features, please see the <a href="/GRNsight/about.html#v1_2Content">About page</a>.</p>
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- <p class="newsHeader">CMSI 402 Senior Project Presentation</p>
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- <p class="newsInfo">Britain Southwick gives a presentation about GRNsight at the Loyola Marymount University CMSI 402 Senior Project Presentations event. Click <a href="http://www.slideshare.net/GRNsight/southwick-britain-grnsightcmsi402presentation20140508" target="_blank">here</a> to view the slides.</p>
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- <p class="newsInfo">Britain Southwick and Nicole Anguiano give a presentation about GRNsight at the <a href="http://academics.lmu.edu/media/lmuacademics/undergraduateresearchsymposium/documents/Full%20Program%20with%20abstracts%203.pdf">Loyola Marymount University 6<sup>th</sup> Annual Undergraduate Research Symposium</a>. Click <a href="http://www.slideshare.net/GRNsight/southwick-anguiano-lmusymposiumpresentation20140329" target="_blank">here</a> to view the slides.</p>
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- <p class="newsHeader">The GRNsight Project is established on GitHub.</p>
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