{"payload":{"pageCount":2,"repositories":[{"type":"Public","name":"mira","owner":"gyorilab","isFork":false,"description":"MIRA modeling framework","allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":4,"issueCount":11,"starsCount":8,"forksCount":6,"license":"BSD 2-Clause \"Simplified\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-06-11T15:20:13.981Z"}},{"type":"Public","name":"trialsynth","owner":"gyorilab","isFork":false,"description":"TrialSynth interprets and integrates clinical trials data from multiple registries in a computable form","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":0,"starsCount":0,"forksCount":1,"license":"BSD 2-Clause \"Simplified\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-06-10T14:53:15.149Z"}},{"type":"Public","name":"adeft","owner":"gyorilab","isFork":false,"description":"Tool for disambiguating acronyms and abbreviations in text for NLP applications","allTopics":["acronym-disambiguation"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":3,"starsCount":20,"forksCount":10,"license":"BSD 2-Clause \"Simplified\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-06-10T13:28:42.600Z"}},{"type":"Public","name":"emmaa","owner":"gyorilab","isFork":false,"description":"Ecosystem of Machine-maintained Models with Automated Analysis","allTopics":["cancer","biology","modeling","systems-biology","systems-biology-simulation","indra"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":4,"issueCount":1,"starsCount":10,"forksCount":10,"license":"BSD 2-Clause \"Simplified\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-06-08T01:20:01.400Z"}},{"type":"Public","name":"indra_cogex","owner":"gyorilab","isFork":false,"description":"INDRA Context Graph Extension","allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":4,"issueCount":16,"starsCount":6,"forksCount":8,"license":"BSD 2-Clause \"Simplified\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-06-08T00:17:00.259Z"}},{"type":"Public","name":"ui_util","owner":"gyorilab","isFork":false,"description":"This repo creates general utilities for our user interfaces.","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":2,"issueCount":0,"starsCount":0,"forksCount":4,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-06-07T23:40:52.991Z"}},{"type":"Public","name":"gyorilab.github.io","owner":"gyorilab","isFork":false,"description":"Gyori Lab website","allTopics":[],"primaryLanguage":{"name":"JavaScript","color":"#f1e05a"},"pullRequestCount":0,"issueCount":0,"starsCount":3,"forksCount":3,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-06-05T14:33:00.400Z"}},{"type":"Public","name":"indra_signor","owner":"gyorilab","isFork":false,"description":"Connecting INDRA to the SIGNOR database curation workflow","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-06-04T15:52:37.855Z"}},{"type":"Public","name":"outbreak_kg","owner":"gyorilab","isFork":false,"description":"Knowledge graphs for disease outbreak scenarios","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-31T17:55:37.736Z"}},{"type":"Public","name":"neuroimmune_interactome","owner":"gyorilab","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"HTML","color":"#e34c26"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-13T18:44:58.840Z"}},{"type":"Public","name":"indra_may_institute","owner":"gyorilab","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":1,"starsCount":1,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-12T19:06:13.946Z"}},{"type":"Public","name":"pybiopax","owner":"gyorilab","isFork":false,"description":"PyBioPAX: A python implementation of the BioPAX object model","allTopics":["biology","systems-biology","biopax","python"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":1,"starsCount":23,"forksCount":6,"license":"BSD 2-Clause \"Simplified\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-10T20:49:19.894Z"}},{"type":"Public","name":"gilda","owner":"gyorilab","isFork":false,"description":"Grounding of biomedical named entities with contextual disambiguation","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":4,"issueCount":8,"starsCount":36,"forksCount":8,"license":"BSD 2-Clause \"Simplified\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-09T04:11:27.374Z"}},{"type":"Public","name":"protmapper_paper","owner":"gyorilab","isFork":false,"description":"Code to generate results and figures relevant to the ProtMapper manuscript.","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-08T03:53:30.989Z"}},{"type":"Public","name":"indra_network_search","owner":"gyorilab","isFork":false,"description":"REST API for querying the network of biochemical mechanisms in the INDRA DB.","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":12,"starsCount":0,"forksCount":2,"license":"BSD 2-Clause \"Simplified\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-05T22:06:52.382Z"}},{"type":"Public","name":"indra_db","owner":"gyorilab","isFork":false,"description":"A Database-based knowledge back-end built on and for INDRA. The INDRA Database is a service that can be set up by any user with their own content and knowledge access. Our implementation of the database is the back-end to many of our projects, providing a vast and detailed knowledge base derived from many resources.","allTopics":["sqlalchemy","database","systems-biology","postgresql","indra","machine-reading"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":3,"issueCount":6,"starsCount":16,"forksCount":9,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-03-12T13:29:47.921Z"}},{"type":"Public","name":"opaque","owner":"gyorilab","isFork":false,"description":"Outlier Prevalence Analysis for Quantification of Unknown Entities","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":1,"license":"BSD 2-Clause \"Simplified\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-03-04T19:15:45.470Z"}},{"type":"Public","name":"protmapper","owner":"gyorilab","isFork":false,"description":"Map amino acid sites of post-translational modifications from models or data to reference positions.","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":5,"forksCount":7,"license":"BSD 2-Clause \"Simplified\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-01-19T04:49:39.361Z"}},{"type":"Public","name":"indra_db_lite","owner":"gyorilab","isFork":false,"description":"Work with content from indra_db in a local sqlite database.","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":2,"license":"BSD 2-Clause \"Simplified\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-11-26T14:56:58.953Z"}},{"type":"Public","name":"indra_reading","owner":"gyorilab","isFork":false,"description":"Tools used for large scale reading, mostly using AWS Batch.","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":0,"starsCount":0,"forksCount":5,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-10-11T18:19:17.977Z"}},{"type":"Public","name":"covid-19","owner":"gyorilab","isFork":false,"description":"Scripts and other utilities relevant to the CORD-19 dataset","allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":2,"issueCount":0,"starsCount":1,"forksCount":4,"license":"BSD 2-Clause \"Simplified\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-06-20T16:56:13.428Z"}},{"type":"Public","name":"indra_curation","owner":"gyorilab","isFork":false,"description":"A utility build around the HTML assembler to enable easy curation of custom sets of INDRA Statements.","allTopics":[],"primaryLanguage":{"name":"JavaScript","color":"#f1e05a"},"pullRequestCount":0,"issueCount":1,"starsCount":0,"forksCount":4,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-06-17T23:46:28.278Z"}},{"type":"Public","name":"go_networks","owner":"gyorilab","isFork":false,"description":"INDRA-assembled networks of mechanisms between genes sets corresponding to GO terms","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-06-08T20:56:11.785Z"}},{"type":"Public","name":"indra_world","owner":"gyorilab","isFork":false,"description":"INDRA World Modelers services","allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":6,"forksCount":5,"license":"BSD 2-Clause \"Simplified\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-02-28T00:59:12.317Z"}},{"type":"Public","name":"indralab-vue","owner":"gyorilab","isFork":false,"description":"A package of Vue Components for use in Indralab web services.","allTopics":[],"primaryLanguage":{"name":"Vue","color":"#41b883"},"pullRequestCount":23,"issueCount":0,"starsCount":0,"forksCount":3,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-01-06T02:29:48.318Z"}},{"type":"Public","name":"panacea_indra","owner":"gyorilab","isFork":false,"description":"INDRA applications for the DARPA Panacea project","allTopics":[],"primaryLanguage":{"name":"HTML","color":"#e34c26"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":2,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-11-07T16:25:32.612Z"}},{"type":"Public","name":"causal_precedence_training","owner":"gyorilab","isFork":false,"description":"Scripts for assembling datasets for causal precedence prediction","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":0,"starsCount":0,"forksCount":3,"license":"BSD 2-Clause \"Simplified\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-11-03T06:30:21.599Z"}},{"type":"Public","name":"depmap_analysis","owner":"gyorilab","isFork":true,"description":"","allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":7,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-08-12T05:26:13.598Z"}},{"type":"Public","name":"indra_spine","owner":"gyorilab","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-07-23T01:57:59.261Z"}},{"type":"Public","name":"adeft_indra","owner":"gyorilab","isFork":false,"description":"Build Adeft models with content from the INDRA Database","allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"BSD 2-Clause \"Simplified\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-05-21T03:21:06.952Z"}}],"repositoryCount":47,"userInfo":null,"searchable":true,"definitions":[],"typeFilters":[{"id":"all","text":"All"},{"id":"public","text":"Public"},{"id":"source","text":"Sources"},{"id":"fork","text":"Forks"},{"id":"archived","text":"Archived"},{"id":"template","text":"Templates"}],"compactMode":false},"title":"Repositories"}