grnsight 6.0.4 → 6.0.7

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 (1197) hide show
  1. package/database/README.md +40 -16
  2. package/database/expression-database/README.md +2 -2
  3. package/database/expression-database/schema.sql +14 -14
  4. package/database/expression-database/scripts/loader.py +6 -6
  5. package/database/network-database/README.md +36 -4
  6. package/database/network-database/schema.sql +7 -7
  7. package/database/network-database/scripts/filter_genes.py +1 -1
  8. package/database/network-database/scripts/generate_network.py +1 -1
  9. package/database/network-database/scripts/generate_new_network_version.py +223 -0
  10. package/database/network-database/scripts/loader.py +3 -3
  11. package/database/network-database/scripts/loader_updates.py +99 -0
  12. package/package.json +2 -2
  13. package/server/controllers/custom-workbook-controller.js +4 -3
  14. package/server/dals/expression-dal.js +8 -7
  15. package/server/dals/network-dal.js +3 -3
  16. package/web-client/public/js/api/grnsight-api.js +56 -55
  17. package/web-client/public/js/generateNetwork.js +15 -7
  18. package/web-client/public/js/setup-load-and-import-handlers.js +171 -170
  19. package/web-client/public/js/upload.js +74 -95
  20. package/.bundle/config +0 -3
  21. package/GRNsight - Beta.html +0 -194
  22. package/Gemfile.lock +0 -259
  23. package/_gh_pages/about.html +0 -807
  24. package/_gh_pages/assets/css/bootstrap.min.css +0 -10
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- <p class="newsDate">June 7, 2019</p>
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- <p class="newsInfo">Kam D. Dahlquist, John David N. Dionisio, Ben G. Fitzpatrick, Nicole A. Anguiano, Anindita Varshneya, Britain J. Southwick, Mihir Samdarshi. (2016) GRNsight: a web application and service for visualizing models of small- to medium-scale gene regulatory networks. <em>PeerJ Computer Science</em> 2:e85 <a href="https://doi.org/10.7717/peerj-cs.85" target="_blank">https://doi.org/10.7717/peerj-cs.85</a></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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- <p class="newsInfo">GRNsight reached a total of 1,000 file uploads on the website today.</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="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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- <p class="newsDate">March 21, 2015</p>
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- <p class="newsHeader">LMU Undergraduate Research Symposium</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="newsDate">February 25, 2015</p>
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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">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="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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