| HEAD | 3945681 | Remove bogus build status badge | 14 August 2024, 04:54:43 UTC |
| refs/heads/ContextClassifiers | 1d69b90 | passed tests again for running SVM specified in config file | 18 July 2017, 23:39:20 UTC |
| refs/heads/DeepRL | 174c75e | Randomized the order of epochs. Introduced a Decay stream API and implemented Q-Learning | 22 April 2017, 06:59:55 UTC |
| refs/heads/GridSearchParams | 6a4c35b | added breeze dependencies to build.sbt | 18 July 2017, 23:40:36 UTC |
| refs/heads/Jake_Wolfe | 8a61b9c | The smaller baseline window didn't have a big effect on the f1. I'm removing stray prints. | 27 November 2019, 01:03:04 UTC |
| refs/heads/LinearContextEngine | ea330ab | Added denseness information to the cross validation results class | 28 June 2017, 20:01:41 UTC |
| refs/heads/NoBE | 6a21fa7 | Version which eschews Harvard Bioentities resources: (THIS TEST BRANCH ONLY: DO NOT MERGE TO MASTER). | 13 April 2017, 15:59:07 UTC |
| refs/heads/SVMContextEngine | 1183f46 | Added README on how to use the TrainSVMClassifier script and how to configure the SVMContextEngine in application.conf | 21 March 2020, 20:48:00 UTC |
| refs/heads/SortByF1 | 6294dbe | Updated output of Scala SortByScore application to output csv containing: feature_family_subset,(f1, precision, recall, (sparseness_mean, sparseness_SE), (numFeatures_mean, numFeatures_SE)) | 05 July 2017, 22:44:24 UTC |
| refs/heads/addNegativeLookaround | 809c618 | Add unrestricted negative around for simple event rule | 23 March 2016, 19:50:26 UTC |
| refs/heads/all-fries_160314 | 2808702 | Save configuration of 13.7K run on 3/14/2016. | 14 March 2016, 18:38:05 UTC |
| refs/heads/all-fries_160331 | 97abfc0 | Save configuration of 16.6K FRIES run on 3/31/2016. | 06 April 2016, 19:50:29 UTC |
| refs/heads/all-ic_160108 | 7772085 | Checkin app config, build file for jenny2 restart part of 291k run, 18-1/14. | 15 January 2016, 01:04:53 UTC |
| refs/heads/alltests | a7cf5a5 | change test aggregation | 18 October 2016, 00:45:29 UTC |
| refs/heads/arabidopsis | c66c95c | Merge branch 'master' into arabidopsis | 27 May 2020, 14:25:39 UTC |
| refs/heads/assembly-is-back | 91dca8c | Added export functionality with assembly | 25 August 2020, 19:35:01 UTC |
| refs/heads/assembly-zhengzhong-20200831 | d294282 | debug | 14 September 2020, 23:13:23 UTC |
| refs/heads/assembly-zhengzhong-20200910 | e604eb8 | try to figure out the labels | 19 September 2020, 03:47:20 UTC |
| refs/heads/assembly-zhengzhong-20200918-annotation | 2183a9c | debug | 31 January 2022, 23:56:30 UTC |
| refs/heads/atcc | 4d07140 | Merge latest 'master' into atcc | 16 September 2016, 23:55:38 UTC |
| refs/heads/bioresources | ef57fe3 | Updated the instructions | 07 April 2021, 23:18:57 UTC |
| refs/heads/bioresources_build | 4790865 | Add bioresources to build | 18 October 2023, 02:06:11 UTC |
| refs/heads/brat-fix | c322852 | Addresses #383 | 09 December 2016, 05:02:41 UTC |
| refs/heads/cardexport | 7e4a9c0 | Add transport/translocation. | 05 May 2015, 20:40:11 UTC |
| refs/heads/context | 0dc72d5 | Restored the standoff functionality to the context output | 15 February 2017, 02:08:34 UTC |
| refs/heads/context-balancing | 6c29002 | deleted CtxID and EvtID from df in logistic_CV_by_paper.py | 19 September 2017, 17:56:05 UTC |
| refs/heads/context_module | 7773b67 | Added the files for feature extraction and the scafolding code to train the svm classifier and the skeleton of the SVM context engine | 09 February 2021, 01:10:38 UTC |
| refs/heads/context_zhengzhong_20220510_pytorch | 40d0f85 | done with cotraining code | 15 May 2022, 05:44:09 UTC |
| refs/heads/context_zhengzhong_idf | a8964c2 | test keyword idf score | 19 November 2019, 02:22:07 UTC |
| refs/heads/corefBrat | 4b963e5 | Add 'which' to 'X which is MODIFIED' PTM rules | 17 February 2016, 20:38:21 UTC |
| refs/heads/corenlp-to-fastnlp | 04bcce1 | Use processors fastnlp-bio branch | 14 December 2016, 22:26:35 UTC |
| refs/heads/crop | c11761b | added some crop keywords | 23 October 2017, 18:16:43 UTC |
| refs/heads/data-root | 3a4acae | Set root dir to /data for building Docker images. | 07 May 2019, 03:56:09 UTC |
| refs/heads/dengue | 972981e | More queries for dengue use case | 03 March 2017, 17:56:36 UTC |
| refs/heads/dockerize | 93e81ab | docker external files | 08 June 2018, 04:27:51 UTC |
| refs/heads/dsv-parser-encoding | db7a1c7 | Merge latest 'master' into dsv-parser-encoding | 30 August 2016, 00:36:43 UTC |
| refs/heads/e2f | 02a5359 | Added test for E2F | 21 September 2016, 14:10:27 UTC |
| refs/heads/edin | cbd116f | Some triggers may be shared by different events | 03 March 2019, 02:37:36 UTC |
| refs/heads/enoriega/training_output | ed0b6a7 | Changed the nxml reader version temporarily to a local snapshot | 25 July 2024, 18:47:27 UTC |
| refs/heads/eval13 | 677e8a0 | Transcriptions do not have controllers | 25 June 2018, 21:23:07 UTC |
| refs/heads/eval13-trigger-reuse | a9cdbe9 | No repeat triggers | 20 June 2018, 21:01:36 UTC |
| refs/heads/fastbio | 9d8740a | Fixed syntax_7_noun for pos/neg regs | 21 February 2017, 23:08:14 UTC |
| refs/heads/fb2 | 536225c | added test | 25 July 2016, 18:43:39 UTC |
| refs/heads/fix_target_of | fd946e5 | Exclude target from copula rule | 20 August 2018, 16:00:15 UTC |
| refs/heads/fix_transcription | 7ea49e5 | Add test for flipped transcription_0 rule | 06 March 2020, 22:35:54 UTC |
| refs/heads/fr-temporary | 3967e7a | Temporarely changed CMURow.scala line 289 to export the species context into the "Organism" column, instead of the organ context | 16 November 2017, 05:13:03 UTC |
| refs/heads/frailty | 0f07901 | Added terms for Skye's search | 06 December 2022, 19:45:47 UTC |
| refs/heads/gh-pages | f7e0013 | updated site | 01 April 2016, 04:40:29 UTC |
| refs/heads/gna | bef217c | Dependent on next Bioresources (currently snapshot). | 07 December 2016, 00:31:31 UTC |
| refs/heads/i16 | 4fcaa39 | Add tests of some subcellular location overrides. Requires BR 1.1.23 commit 3d7ed7e or later. | 16 February 2017, 21:58:30 UTC |
| refs/heads/issue124 | 3b9609e | Start altering alias | 31 March 2016, 20:39:06 UTC |
| refs/heads/keywords | f5489f6 | Split the queries in different files | 19 April 2022, 20:15:07 UTC |
| refs/heads/kwalcock-loop | d7507e7 | Include Mutants | 05 February 2021, 15:45:42 UTC |
| refs/heads/kwalcock/javaCheck | e61f7c8 | Check java version number | 17 February 2021, 01:16:58 UTC |
| refs/heads/kwalcock/json | d13b738 | Remove equivalenceHashes when finished with Document | 04 March 2023, 00:05:28 UTC |
| refs/heads/kwalcock/modernize | a36d144 | Make it build | 30 June 2022, 18:36:03 UTC |
| refs/heads/kwalcock/processorsGlove | 986e8bd | Update to processors 8.3.1 | 06 April 2021, 16:57:59 UTC |
| refs/heads/kwalcock/rehash | 46f81e2 | Prepare for processors update autoclose, java converters, sbt version | 20 July 2023, 17:25:13 UTC |
| refs/heads/kwalcock/rejson | ab4aa61 | Add output | 31 March 2023, 16:23:55 UTC |
| refs/heads/kwalcock/updateCommon | d41d91c | Update builds | 24 March 2023, 20:50:58 UTC |
| refs/heads/master | 3945681 | Remove bogus build status badge | 14 August 2024, 04:54:43 UTC |
| refs/heads/mastmeas | 802f288 | Pull gref measurement branch into master measurement branch. | 22 February 2017, 19:39:10 UTC |
| refs/heads/mayank | d9196f6 | Added sample script and a random paper to test the script to demonstrate REACH's API to Mayank | 07 November 2023, 22:36:29 UTC |
| refs/heads/megha | 3b04d68 | Added use case. | 24 April 2018, 17:31:25 UTC |
| refs/heads/new-events | 1678be4 | Use select Translocation rules for Localization | 02 March 2019, 03:46:48 UTC |
| refs/heads/new-events-futures | 86eacbe | Future-based concurrency model for ReachCLI Try to avoid wasting resources when encountering a hanging paper | 02 March 2019, 06:07:47 UTC |
| refs/heads/nmz_151209 | 82cc5bc | Increase memory via SBT. | 09 December 2015, 22:18:14 UTC |
| refs/heads/path_filter | 70ca0d4 | Initial attempt from Enrique at mention filters | 03 December 2018, 22:26:23 UTC |
| refs/heads/phase3 | eca33e9 | Update build file to use processors 6.0.2 release. | 08 February 2017, 00:54:31 UTC |
| refs/heads/phospho | 50659d0 | New script | 16 November 2018, 23:05:43 UTC |
| refs/heads/polarity_engine_20200104 | 02d4ea3 | debug | 14 January 2020, 05:27:07 UTC |
| refs/heads/polarity_engine_20200113 | 5fb34ba | debug | 15 January 2020, 21:29:41 UTC |
| refs/heads/polarity_engine_full | 366f65d | debug | 01 July 2019, 20:39:25 UTC |
| refs/heads/proc620 | 7cd30b1 | WIP First attempt at switching to odin.Modification and Mention.modifications | 30 November 2017, 05:48:52 UTC |
| refs/heads/proctest | 06a1475 | Merge branch 'master' into proctest | 20 October 2017, 15:43:12 UTC |
| refs/heads/projectb | fbf30d3 | Added usecase7 | 02 April 2016, 03:53:21 UTC |
| refs/heads/readme-patch | 3dfbdbc | Update README.md Declared support for Java 11 | 27 January 2021, 18:59:18 UTC |
| refs/heads/regCreg | 6f1c1d9 | Make build use BR 1.1.10; last version before 5-col reformatting. | 10 July 2016, 20:16:10 UTC |
| refs/heads/reload | 942f610 | Fixed theh bugs that broke the tests | 07 September 2018, 21:53:28 UTC |
| refs/heads/revert-421-issue352 | 5086925 | Revert "Removed ambiguous binding rule." | 26 October 2016, 09:53:59 UTC |
| refs/heads/rexport | 7d9a577 | Merge big new shiney master branch. | 13 May 2015, 22:42:39 UTC |
| refs/heads/scala2.12 | 21c0042 | WIP: begin mods to scala 2.12. Does not yet compile. | 07 December 2017, 19:43:01 UTC |
| refs/heads/serialize-this | 987a4d9 | Serialize nxml papers to Document json | 15 December 2016, 18:16:55 UTC |
| refs/heads/sri | 38be579 | Rename build artifacts for this branch to avoid confusion. | 13 September 2017, 18:19:16 UTC |
| refs/heads/tair | 9bab4f5 | Merge branch 'master' into tair | 09 May 2018, 22:06:42 UTC |
| refs/heads/test_hgnc | 2be885a | Integrate human gene synonyms from HGNC | 26 March 2020, 13:27:37 UTC |
| refs/heads/token_rule | 1aae738 | preliminary work on simple event edge case (token of rule) | 05 February 2019, 17:05:52 UTC |
| refs/heads/trigger-tweaks | 3be56c4 | Less noisy Gene Expression triggers | 01 March 2019, 00:44:17 UTC |
| refs/heads/ud_with_variables | 16e53e8 | added dep var | 03 November 2018, 07:04:54 UTC |
| refs/heads/unpack-for-output | 6041b46 | Silence! | 17 August 2016, 21:32:47 UTC |
| refs/heads/vikas_micro | 6125c4b | Update NxmlSearcher.scala | 18 December 2017, 07:24:38 UTC |
| refs/heads/webapp_collect_args | 354afe7 | added comment to the method Enrique wrote; deleted the unused code | 29 January 2019, 20:32:51 UTC |
| refs/heads/zain | eae966b | New queries for afib | 26 March 2018, 20:18:35 UTC |
| refs/tags/1.0.1-SNAPSHOT | a840b02 | Started 1.0.1-SNAPSHOT. | 30 September 2015, 03:14:09 UTC |
| refs/tags/1.1.0-SNAPSHOT | 98652a5 | Started 1.1.0-SNAPSHOT. | 16 October 2015, 21:44:10 UTC |
| refs/tags/291k-run_160108 | 60e8e26 | Added Pandas output as a choice in ReachCLI | 06 January 2016, 23:44:08 UTC |
| refs/tags/PullRequest_64 | 6ce4d56 | Merge branch 'master' into ground4. | 12 February 2016, 21:20:59 UTC |
| refs/tags/Release-1.1.1 | d6705c1 | Prepared 1.1.1 | 28 October 2015, 03:59:29 UTC |
| refs/tags/Release-1.1.2 | bb232a3 | Prepared 1.1.2 release. | 07 November 2015, 03:15:26 UTC |
| refs/tags/Release_1.2.2 | 6ad8485 | Prepared 1.2.2 release. | 26 January 2016, 17:33:11 UTC |
