grnsight 4.0.0 → 6.0.0
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.
- package/.travis.yml +3 -1
- package/GRNsight - Beta.html +194 -0
- package/Gemfile.lock +259 -0
- package/README.md +2 -2
- package/_gh_pages/about.html +360 -45
- package/_gh_pages/assets/css/footer.css +3 -0
- package/_gh_pages/assets/css/main.css +28 -14
- package/_gh_pages/assets/images/21-genes_31-edges_Schade-data_estimation_output_binary-no-targetless-genes_sif.png +0 -0
- package/_gh_pages/assets/images/21-genes_31-edges_Schade-data_estimation_output_binary_sif.png +0 -0
- package/_gh_pages/assets/images/21-genes_31-edges_Schade-data_graphml_3-edges-and-footer.png +0 -0
- package/_gh_pages/assets/images/21-genes_31-edges_Schade-data_graphml_header-and-3-nodes.png +0 -0
- package/_gh_pages/assets/images/21-genes_31-edges_Schade-data_graphml_output_3-edges-and-footer.png +0 -0
- package/_gh_pages/assets/images/21-genes_31-edges_Schade-data_graphml_output_header-and-3-nodes.png +0 -0
- package/_gh_pages/assets/images/21-genes_31-edges_Schade-data_input_binary-no-targetless-genes_sif.png +0 -0
- package/_gh_pages/assets/images/21-genes_31-edges_Schade-data_input_binary_sif.png +0 -0
- package/_gh_pages/assets/images/21-genes_31-edges_Schade-data_input_concatenated-no-targetless-genes_sif.png +0 -0
- package/_gh_pages/assets/images/21-genes_31-edges_Schade-data_input_concatenated_sif.png +0 -0
- package/_gh_pages/assets/images/Choe-Shin_CMSI402-poster-session_20180430.jpg +0 -0
- package/_gh_pages/assets/images/Choe_SCCUR_2017.jpg +0 -0
- package/_gh_pages/assets/images/Dahlquist-Choe-Shin_CMSI402-poster-session_20180430.jpg +0 -0
- package/_gh_pages/assets/images/Dionisio-Dahlquist_GRNsight-shades_20170506.jpg +0 -0
- package/_gh_pages/assets/images/Klein_Samdarshi_TriBeta_2018_20180317.jpg +0 -0
- package/_gh_pages/assets/images/Shin_SCCUR_2017.jpg +0 -0
- package/{documents/manuscripts/peerj-computerscience-2016/figures/submitted-versions/Figure1_zoom145_900pix-wide.png → _gh_pages/assets/images/demo-3_network-sheet.png} +0 -0
- package/{documents/manuscripts/peerj-computerscience-2016/figures/submitted-versions/Figure2_zoom145_900pix-wide.png → _gh_pages/assets/images/demo-4_network-optimized-weights-sheet.png} +0 -0
- package/_gh_pages/assets/images/gene-pages-0.png +0 -0
- package/_gh_pages/assets/images/gene-pages-1.png +0 -0
- package/_gh_pages/assets/images/gene-pages-2.png +0 -0
- package/_gh_pages/assets/images/gene-pages-3.png +0 -0
- package/_gh_pages/assets/images/grnsight2020.png +0 -0
- package/_gh_pages/assets/images/v3demo2-grid+nodecoloring.png +0 -0
- package/_gh_pages/assets/images/v3demo2-nodecoloring.png +0 -0
- package/_gh_pages/assets/images/v3demo2.png +0 -0
- package/_gh_pages/assets/js/ga-report.js +11 -11
- package/_gh_pages/assets/js/iframeResizer.min.js +9 -0
- package/_gh_pages/assets/js/main.js +43 -43
- package/_gh_pages/beta.html +29 -24
- package/_gh_pages/contact.html +31 -31
- package/_gh_pages/coverage/coverage.json +1 -0
- package/_gh_pages/coverage/coverage.raw.json +1 -0
- package/_gh_pages/coverage/lcov-report/base.css +223 -0
- package/_gh_pages/coverage/lcov-report/block-navigation.js +63 -0
- package/_gh_pages/coverage/lcov-report/controllers/additional-sheet-parser.js.html +330 -0
- package/_gh_pages/coverage/lcov-report/controllers/constants.js.html +243 -0
- package/_gh_pages/coverage/lcov-report/controllers/export-controller.js.html +285 -0
- package/_gh_pages/coverage/lcov-report/controllers/exporters/graphml.js.html +405 -0
- package/_gh_pages/coverage/lcov-report/controllers/exporters/index.html +110 -0
- package/_gh_pages/coverage/lcov-report/controllers/exporters/sif.js.html +150 -0
- package/_gh_pages/coverage/lcov-report/controllers/helpers.js.html +114 -0
- package/_gh_pages/coverage/lcov-report/controllers/import-controller.js.html +233 -0
- package/_gh_pages/coverage/lcov-report/controllers/importers/graphml.js.html +716 -0
- package/_gh_pages/coverage/lcov-report/controllers/importers/index.html +106 -0
- package/_gh_pages/coverage/lcov-report/controllers/importers/sif.js.html +488 -0
- package/_gh_pages/coverage/lcov-report/controllers/index.html +162 -0
- package/_gh_pages/coverage/lcov-report/controllers/semantic-checker.js.html +810 -0
- package/_gh_pages/coverage/lcov-report/controllers/spreadsheet-controller.js.html +1779 -0
- package/_gh_pages/coverage/lcov-report/index.html +136 -0
- package/_gh_pages/coverage/lcov-report/prettify.css +1 -0
- package/_gh_pages/coverage/lcov-report/prettify.js +1 -0
- package/_gh_pages/coverage/lcov-report/server/controllers/additional-sheet-parser.js.html +330 -0
- package/_gh_pages/coverage/lcov-report/server/controllers/constants.js.html +243 -0
- package/_gh_pages/coverage/lcov-report/server/controllers/export-controller.js.html +285 -0
- package/_gh_pages/coverage/lcov-report/server/controllers/exporters/graphml.js.html +405 -0
- package/_gh_pages/coverage/lcov-report/server/controllers/exporters/index.html +110 -0
- package/_gh_pages/coverage/lcov-report/server/controllers/exporters/sif.js.html +150 -0
- package/_gh_pages/coverage/lcov-report/server/controllers/graphml-constants.js.html +585 -0
- package/_gh_pages/coverage/lcov-report/server/controllers/helpers.js.html +114 -0
- package/_gh_pages/coverage/lcov-report/server/controllers/import-controller.js.html +237 -0
- package/_gh_pages/coverage/lcov-report/server/controllers/importers/graphml.js.html +585 -0
- package/_gh_pages/coverage/lcov-report/server/controllers/importers/index.html +110 -0
- package/_gh_pages/coverage/lcov-report/server/controllers/importers/sif.js.html +492 -0
- package/_gh_pages/coverage/lcov-report/server/controllers/index.html +188 -0
- package/_gh_pages/coverage/lcov-report/server/controllers/semantic-checker.js.html +810 -0
- package/_gh_pages/coverage/lcov-report/server/controllers/spreadsheet-controller.js.html +1779 -0
- package/_gh_pages/coverage/lcov-report/sort-arrow-sprite.png +0 -0
- package/_gh_pages/coverage/lcov-report/sorter.js +158 -0
- package/_gh_pages/coverage/lcov-report/web-client/public/js/grnstate.js.html +225 -0
- package/_gh_pages/coverage/lcov-report/web-client/public/js/index.html +97 -0
- package/_gh_pages/coverage/lcov.info +49 -0
- package/_gh_pages/documentation.html +998 -320
- package/_gh_pages/documents/abstracts/SIGGRAPH 2017 Abstract/siggraph-abstract-review.aux +47 -0
- package/_gh_pages/documents/abstracts/SIGGRAPH 2017 Abstract/siggraph-abstract-review.bbl +73 -0
- package/_gh_pages/documents/abstracts/SIGGRAPH 2017 Abstract/siggraph-abstract-review.blg +52 -0
- package/_gh_pages/documents/abstracts/SIGGRAPH 2017 Abstract/siggraph-abstract-review.log +1056 -0
- package/_gh_pages/documents/abstracts/SIGGRAPH 2017 Abstract/siggraph-abstract-review.out +7 -0
- package/_gh_pages/documents/abstracts/SIGGRAPH 2017 Abstract/siggraph-abstract-review.synctex.gz +0 -0
- package/_gh_pages/documents/manuscripts/peerj-computerscience-2016/revisions/GRNsight_PeerJ-CS_manuscript_2016_text-only_revised-Dondi.docx +0 -0
- package/_gh_pages/encryption/server.cert +21 -0
- package/_gh_pages/encryption/server.key +28 -0
- package/_gh_pages/favicon.ico +0 -0
- package/_gh_pages/index.html +45 -22
- package/_gh_pages/links.html +47 -28
- package/_gh_pages/news.html +103 -21
- package/_gh_pages/onlyfooter.html +78 -0
- package/_gh_pages/onlyheader.html +64 -0
- package/_gh_pages/onlysidebar.html +73 -0
- package/_gh_pages/package-lock.json +14048 -0
- package/_gh_pages/people.html +129 -40
- package/_gh_pages/privacy.html +23 -17
- package/_gh_pages/publications.html +75 -33
- package/_gh_pages/robots.txt +1 -0
- package/_gh_pages/sitemap.xml +87 -74
- package/_gh_pages/test-files/import-samples/attributes.graphml +40 -0
- package/_gh_pages/test-files/import-samples/port.graphml +32 -0
- package/_gh_pages/test-files/import-samples/simple.graphml +31 -0
- package/_gh_pages/web-client/public/js/grnsight.min.js +2347 -0
- package/_gh_pages/web-client/public/stylesheets/grnsight.css +443 -0
- package/coverage/coverage.json +1 -1
- package/coverage/lcov.info +1847 -1142
- package/database/README.md +1 -0
- package/database/network-database/README.md +44 -0
- package/database/network-database/schema.sql +24 -0
- package/database/network-database/scripts/filter_genes.py +76 -0
- package/database/network-database/scripts/generate_network.py +199 -0
- package/database/network-database/scripts/generate_sgd_network_from_yeastract_network.py +120 -0
- package/database/network-database/scripts/loader.py +78 -0
- package/package.json +20 -11
- package/server/app.js +7 -2
- package/server/config/config.js +12 -3
- package/server/controllers/additional-sheet-parser.js +292 -55
- package/server/controllers/constants.js +4 -37
- package/server/controllers/custom-workbook-controller.js +66 -0
- package/server/controllers/demo-workbooks.js +5973 -0
- package/server/controllers/export-constants.js +78 -0
- package/server/controllers/export-controller.js +4 -3
- package/server/controllers/exporters/graphml.js +15 -15
- package/server/controllers/exporters/sif.js +7 -7
- package/server/controllers/exporters/xlsx.js +110 -34
- package/server/controllers/expression-database-controller.js +19 -0
- package/server/controllers/expression-sheet-parser.js +170 -0
- package/server/controllers/graphml-constants.js +0 -17
- package/server/controllers/helpers.js +25 -1
- package/server/controllers/import-controller.js +2 -2
- package/server/controllers/importers/graphml.js +17 -20
- package/server/controllers/importers/sif.js +22 -18
- package/server/controllers/network-database-controller.js +18 -0
- package/server/controllers/network-sheet-parser.js +307 -0
- package/server/controllers/semantic-checker.js +30 -162
- package/server/controllers/sif-constants.js +36 -0
- package/server/controllers/spreadsheet-controller.js +277 -425
- package/server/controllers/workbook-constants.js +521 -0
- package/server/dals/expression-dal.js +122 -0
- package/server/dals/network-dal.js +96 -0
- package/test/additional-sheet-parser-tests.js +147 -38
- package/test/api-tests.js +3 -6
- package/test/errors-adjacency-matrix-modifications.js +30 -29
- package/test/errors-graph-tests.js +4 -4
- package/test/errors-sheet-modifications.js +10 -2
- package/test/export-tests.js +187 -60
- package/test/expression-data-import-tests.js +113 -0
- package/test/grnstate-tests.js +8 -2
- package/test/import-graphml-tests.js +59 -40
- package/test/import-sif-tests.js +50 -37
- package/test/test.js +554 -91
- package/test/warnings-adjacency-matrix-modifications.js +8 -7
- package/test-files/additional-sheet-test-files/optimization-diagnostics-default.xlsx +0 -0
- package/test-files/additional-sheet-test-files/optimization-diagnostics-extraneous-data.xlsx +0 -0
- package/test-files/additional-sheet-test-files/optimization-diagnostics-incorrect-MSE-gene-header.xlsx +0 -0
- package/test-files/additional-sheet-test-files/optimization-diagnostics-incorrect-MSE-header.xlsx +0 -0
- package/test-files/additional-sheet-test-files/optimization-diagnostics-incorrect-column-headers.xlsx +0 -0
- package/test-files/additional-sheet-test-files/optimization-diagnostics-invalid-MSE-data.xlsx +0 -0
- package/test-files/additional-sheet-test-files/optimization-diagnostics-invalid-value.xlsx +0 -0
- package/test-files/additional-sheet-test-files/optimization-diagnostics-missing-MSE-data.xlsx +0 -0
- package/test-files/additional-sheet-test-files/optimization-diagnostics-missing-column-headers.xlsx +0 -0
- package/test-files/additional-sheet-test-files/optimization-diagnostics-missing-header.xlsx +0 -0
- package/test-files/additional-sheet-test-files/optimization-diagnostics-unknown-parameter.xlsx +0 -0
- package/test-files/additional-sheet-test-files/optimization-parameters-default.xlsx +0 -0
- package/test-files/additional-sheet-test-files/optimization-parameters-incorrect-headers.xlsx +0 -0
- package/test-files/additional-sheet-test-files/optimization-parameters-invalid-optimization-parameter.xlsx +0 -0
- package/test-files/additional-sheet-test-files/optimization-parameters-missing-headers.xlsx +0 -0
- package/test-files/additional-sheet-test-files/optimization-parameters-unknown-parameter.xlsx +0 -0
- package/test-files/additional-sheet-test-files/two-column-sheets-extraneous-data.xlsx +0 -0
- package/test-files/additional-sheet-test-files/two-column-sheets-incorrect-cell-A1.xlsx +0 -0
- package/test-files/additional-sheet-test-files/two-column-sheets-incorrect-column-header.xlsx +0 -0
- package/test-files/additional-sheet-test-files/two-column-sheets-invalid-gene-length.xlsx +0 -0
- package/test-files/additional-sheet-test-files/two-column-sheets-invalid-gene-type.xlsx +0 -0
- package/test-files/additional-sheet-test-files/two-column-sheets-invalid-value.xlsx +0 -0
- package/test-files/additional-sheet-test-files/two-column-sheets-missing-column-header.xlsx +0 -0
- package/test-files/additional-sheet-test-files/two-column-sheets-special-character.xlsx +0 -0
- package/test-files/adjacency-matrix-modifications/asymmetric-gene-order-input.xlsx +0 -0
- package/test-files/adjacency-matrix-modifications/asymmetric-gene-order-output.xlsx +0 -0
- package/test-files/adjacency-matrix-modifications/extra-column-adjacent-input.xlsx +0 -0
- package/test-files/adjacency-matrix-modifications/extra-column-adjacent-output.xlsx +0 -0
- package/test-files/adjacency-matrix-modifications/extra-column-end-of-sheet-input.xlsx +0 -0
- package/test-files/adjacency-matrix-modifications/extra-column-end-of-sheet-output.xlsx +0 -0
- package/test-files/adjacency-matrix-modifications/extra-data-random-cell-both-output.xlsx +0 -0
- package/test-files/adjacency-matrix-modifications/extra-data-random-cell-network-only-input.xlsx +0 -0
- package/test-files/adjacency-matrix-modifications/extra-data-random-cell-network-only-output.xlsx +0 -0
- package/test-files/adjacency-matrix-modifications/extra-data-random-cell-network-optimized-only-output.xlsx +0 -0
- package/test-files/adjacency-matrix-modifications/extra-row-end-of-sheet-input.xlsx +0 -0
- package/test-files/adjacency-matrix-modifications/extra-row-end-of-sheet-output.xlsx +0 -0
- package/test-files/adjacency-matrix-modifications/incorrect-network-cell-A1.xlsx +0 -0
- package/test-files/adjacency-matrix-modifications/missing-column-end-input.xlsx +0 -0
- package/test-files/adjacency-matrix-modifications/missing-column-end-output.xlsx +0 -0
- package/test-files/adjacency-matrix-modifications/missing-data-input.xlsx +0 -0
- package/test-files/adjacency-matrix-modifications/missing-data-output.xlsx +0 -0
- package/test-files/adjacency-matrix-modifications/missing-row-end-input.xlsx +0 -0
- package/test-files/adjacency-matrix-modifications/missing-row-end-output.xlsx +0 -0
- package/test-files/adjacency-matrix-modifications/missing-row-middle-input.xlsx +0 -0
- package/test-files/adjacency-matrix-modifications/missing-row-middle-output.xlsx +0 -0
- package/test-files/adjacency-matrix-modifications/missing-value-bottom-corner-input.xlsx +0 -0
- package/test-files/adjacency-matrix-modifications/missing-value-bottom-corner-output.xlsx +0 -0
- package/test-files/adjacency-matrix-modifications/value-replaced-w-spaces-both-output.xlsx +0 -0
- package/test-files/adjacency-matrix-modifications/value-replaced-w-spaces-net-only-input.xlsx +0 -0
- package/test-files/adjacency-matrix-modifications/value-replaced-w-spaces-net-op-only-output.xlsx +0 -0
- package/test-files/adjacency-matrix-modifications/value-replaced/342/200/223w-spaces-net-only-output.xlsx +0 -0
- package/test-files/demo-files/15-genes_28-edges_db5_Dahlquist-data_estimation_output.xlsx +0 -0
- package/test-files/demo-files/15-genes_28-edges_db5_Dahlquist-data_input.xlsx +0 -0
- package/test-files/expression-data-test-sheets/expression_sheet_correct_numbering.xlsx +0 -0
- package/test-files/expression-data-test-sheets/expression_sheet_different_number_of_columns.xlsx +0 -0
- package/test-files/expression-data-test-sheets/expression_sheet_empty_column.xlsx +0 -0
- package/test-files/expression-data-test-sheets/expression_sheet_empty_row.xlsx +0 -0
- package/test-files/expression-data-test-sheets/expression_sheet_erroneous_data.xlsx +0 -0
- package/test-files/expression-data-test-sheets/expression_sheet_extra_gene_name.xlsx +0 -0
- package/test-files/expression-data-test-sheets/expression_sheet_incorrectly_ordered_time_points.xlsx +0 -0
- package/test-files/expression-data-test-sheets/expression_sheet_mismatched_case_gene_names.xlsx +0 -0
- package/test-files/expression-data-test-sheets/expression_sheet_mismatched_gene_names.xlsx +0 -0
- package/test-files/expression-data-test-sheets/expression_sheet_missing_column_header.xlsx +0 -0
- package/test-files/expression-data-test-sheets/expression_sheet_missing_data_error.xlsx +0 -0
- package/test-files/expression-data-test-sheets/expression_sheet_missing_data_ok.xlsx +0 -0
- package/test-files/expression-data-test-sheets/expression_sheet_missing_data_ok_export_exact.xlsx +0 -0
- package/test-files/expression-data-test-sheets/expression_sheet_missing_gene_name.xlsx +0 -0
- package/test-files/expression-data-test-sheets/expression_sheet_name_not_in_optparams.xlsx +0 -0
- package/test-files/expression-data-test-sheets/expression_sheet_name_not_present.xlsx +0 -0
- package/test-files/expression-data-test-sheets/expression_sheet_negative_time_points.xlsx +0 -0
- package/test-files/expression-data-test-sheets/expression_sheet_non_numerical_time_points.xlsx +0 -0
- package/test-files/expression-data-test-sheets/expression_sheet_not_existing.xlsx +0 -0
- package/test-files/expression-data-test-sheets/expression_sheet_wrong_id_label.xlsx +0 -0
- package/test-files/expression-data-test-sheets/expression_sheet_wrong_order_gene_names.xlsx +0 -0
- package/test-files/expression-data-test-sheets/expression_sheet_wrong_sheet_name_case.xlsx +0 -0
- package/test-files/expression-data-test-sheets/expression_sheet_wrong_sheet_name_convention.xlsx +0 -0
- package/test-files/gene-name-modifications/NaN-as-gene-name-input.xlsx +0 -0
- package/test-files/gene-name-modifications/NaN-as-gene-name-output.xlsx +0 -0
- package/test-files/gene-name-modifications/mismatched-case-related-input.xlsx +0 -0
- package/test-files/gene-name-modifications/mismatched-case-related-output.xlsx +0 -0
- package/test-files/gene-name-modifications/mismatched-case-unrelated-input.xlsx +0 -0
- package/test-files/gene-name-modifications/mismatched-case-unrelated-output.xlsx +0 -0
- package/test-files/graph-tests/different-sized-networks/{80-genes-0-edges.xlsx → 134-genes-0-edges.xlsx} +0 -0
- package/test-files/graph-tests/different-sized-networks/{45-genes-max-edges.xlsx → 44-source-genes-45-target-genes-max-edges.xlsx} +0 -0
- package/test-files/graph-tests/different-sized-networks/{1-gene-0-edges.xlsx → unused-files/1-gene-0-edges.xlsx} +0 -0
- package/test-files/graph-tests/different-sized-networks/{1-gene-1-edges.xlsx → unused-files/1-gene-1-edges.xlsx} +0 -0
- package/test-files/graph-tests/different-sized-networks/{10-genes-50-edges.xlsx → unused-files/10-genes-50-edges.xlsx} +0 -0
- package/test-files/graph-tests/different-sized-networks/{10-genes-90-edges.xlsx → unused-files/10-genes-90-edges.xlsx} +0 -0
- package/test-files/graph-tests/different-sized-networks/{100-genes-0-edges.xlsx → unused-files/100-genes-0-edges.xlsx} +0 -0
- package/test-files/graph-tests/different-sized-networks/{110-genes-0-edges.xlsx → unused-files/110-genes-0-edges.xlsx} +0 -0
- package/test-files/graph-tests/different-sized-networks/{120-genes-0-edges.xlsx → unused-files/120-genes-0-edges.xlsx} +0 -0
- package/test-files/graph-tests/different-sized-networks/{130-genes-0-edges.xlsx → unused-files/130-genes-0-edges.xlsx} +0 -0
- package/test-files/graph-tests/different-sized-networks/{140-genes-0-edges.xlsx → unused-files/140-genes-0-edges.xlsx} +0 -0
- package/test-files/graph-tests/different-sized-networks/{150-genes-10000-edges.xlsx → unused-files/150-genes-10000-edges.xlsx} +0 -0
- package/test-files/graph-tests/different-sized-networks/{150-genes-20000-edges.xlsx → unused-files/150-genes-20000-edges.xlsx} +0 -0
- package/test-files/graph-tests/different-sized-networks/{150-genes-max-edges.xlsx → unused-files/150-genes-max-edges.xlsx} +0 -0
- package/test-files/graph-tests/different-sized-networks/{160-genes-max-edges.xlsx → unused-files/160-genes-max-edges.xlsx} +0 -0
- package/test-files/graph-tests/different-sized-networks/{20-genes-max-edges.xlsx → unused-files/20-genes-max-edges.xlsx} +0 -0
- package/test-files/graph-tests/different-sized-networks/{25-genes-max-edges.xlsx → unused-files/25-genes-max-edges.xlsx} +0 -0
- package/test-files/graph-tests/different-sized-networks/{30-genes-max-edges.xlsx → unused-files/30-genes-max-edges.xlsx} +0 -0
- package/test-files/graph-tests/different-sized-networks/{34-genes-0-edges.xlsx → unused-files/34-genes-0-edges.xlsx} +0 -0
- package/test-files/graph-tests/different-sized-networks/{34-genes-40-edges.xlsx → unused-files/34-genes-40-edges.xlsx} +0 -0
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\bibcite{peerj}{{2}{2016}{{Dahlquist et~al\unhbox \voidb@x \hbox {.}}}{{Dahlquist, Dionisio, Fitzpatrick, Anguiano, Varshneya, Southwick, and Samdarshi}}}
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\@writefile{toc}{\contentsline {subsection}{\numberline {1.2}Edge Weight Value Display Options}{2}{subsection.1.2}}
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Computer Graphics\/}} \bibinfo{volume}{17}, \bibinfo{number}{12}
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Samdarshi}.} \bibinfo{year}{2016}\natexlab{}.
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visualizing models of small- to medium-scale gene regulatory networks}.
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(There were 2 warnings)
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