{"payload":{"pageCount":1,"repositories":[{"type":"Public","name":"text2model-from-knowledge","owner":"okadalabipr","isFork":false,"description":"Extending BioMASS to construct mathematical models from external knowledge (Arakane et al., 2024)","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":1,"license":"Apache License 2.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-06-09T12:32:28.717Z"}},{"type":"Public","name":"HER2_Cellcycle","owner":"okadalabipr","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-30T14:11:46.941Z"}},{"type":"Public","name":"DynProfiler","owner":"okadalabipr","isFork":true,"description":"","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-27T08:45:29.199Z"}},{"type":"Public","name":"Haga2023","owner":"okadalabipr","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-01-24T07:35:38.803Z"}},{"type":"Public","name":"periodontitis","owner":"okadalabipr","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-06-08T03:52:40.379Z"}},{"type":"Public","name":"inflammatory-aging","owner":"okadalabipr","isFork":false,"description":"Tabata, S. et al.","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-03-09T08:12:24.299Z"}},{"type":"Public","name":"BioMASS.jl","owner":"okadalabipr","isFork":true,"description":"Julia interface to BioMASS, tailored to parameter estimation in systems biology models","allTopics":[],"primaryLanguage":{"name":"Julia","color":"#a270ba"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":2,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-02-28T02:04:43.540Z"}},{"type":"Public","name":"biomass","owner":"okadalabipr","isFork":true,"description":"A Python Framework for Modeling and Analysis of Signaling Systems","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":12,"license":"Apache License 2.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-02-17T01:17:54.491Z"}},{"type":"Public","name":"pasmopy","owner":"okadalabipr","isFork":true,"description":"Patient-Specific Modeling in Python","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":6,"license":"Apache License 2.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-02-16T02:53:35.964Z"}},{"type":"Public","name":"ASURAT","owner":"okadalabipr","isFork":true,"description":"ASURAT: functional annotation-driven unsupervised clustering of single-cell transcriptomes","allTopics":["single-cell-transcriptomics"],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":3,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-01-19T09:35:47.211Z"}},{"type":"Public","name":"Wibisana2021","owner":"okadalabipr","isFork":false,"description":"Imaging and single cell sequencing analyses of super-enhancer activation mediated by NF-κB in B cells (Wibisana, JN et al., 2021)","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":3,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-06-02T02:12:44.996Z"}},{"type":"Public","name":"findfoci","owner":"okadalabipr","isFork":true,"description":"ImageJ2 and R package for quantitative analysis of NF-κB foci","allTopics":[],"primaryLanguage":{"name":"ImageJ Macro","color":"#99AAFF"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":1,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-03-03T02:26:32.481Z"}},{"type":"Public","name":"Ando2021","owner":"okadalabipr","isFork":false,"description":"Ando, M. et al. IκBα is required for full transcriptional induction of some NFκB-regulated genes in response to TNF in MCF-7 cells. npj Syst Biol Appl 7, 42 (2021).","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-01-14T14:57:34.143Z"}},{"type":"Public","name":"ccle_extractor","owner":"okadalabipr","isFork":false,"description":"Python script for extracting dataset from CCLE (Cancer Cell Line Encyclopedia)","allTopics":["python","cancer","pandas","gene-expression","metabolomics","ccle"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":7,"forksCount":3,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-07-15T03:04:48.384Z"}},{"type":"Public","name":"Kanazawa2021","owner":"okadalabipr","isFork":false,"description":"Cell shape‐based chemical screening reveals an epigenetic network mediated by focal adhesions","allTopics":["rna-seq","chip-seq","atac-seq","super-enhancer","go-analysis"],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-03-11T08:01:41.726Z"}},{"type":"Public","name":"Imoto_Cancers_2020","owner":"okadalabipr","isFork":false,"description":"Imoto, H., Zhang, S. & Okada, M. A Computational Framework for Prediction and Analysis of Cancer Signaling Dynamics from RNA Sequencing Data—Application to the ErbB Receptor Signaling Pathway. Cancers (Basel). 12, 2878 (2020).","allTopics":["parameter-estimation","predictive-modeling","breast-cancer","erbb-signaling-network"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2020-10-10T08:40:02.213Z"}},{"type":"Public","name":"Inoue2016","owner":"okadalabipr","isFork":false,"description":"Inoue, K. et al. Oscillation dynamics underlie functional switching of NF-κB for B-cell activation. npj Syst. Biol. Appl. 2, 16024 (2016).","allTopics":["julia","systems-biology","dde","delay-differential-equations","nfkb-dynamics"],"primaryLanguage":{"name":"Julia","color":"#a270ba"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":1,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2020-08-25T01:27:17.111Z"}},{"type":"Public","name":"Imoto2019","owner":"okadalabipr","isFork":false,"description":"Imoto, H. & Okada, M. Signal-dependent regulation of early-response genes and cell cycle: a quantitative view. Curr. Opin. Syst. Biol. 15, 100–108 (2019).","allTopics":["julia","systems-biology","bifurcation","cell-cycle"],"primaryLanguage":{"name":"Julia","color":"#a270ba"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2020-08-25T01:23:52.649Z"}},{"type":"Public","name":"Nakakuki2010","owner":"okadalabipr","isFork":false,"description":"Nakakuki, T. et al. Ligand-specific c-Fos expression emerges from the spatiotemporal control of ErbB network dynamics. Cell 141, 884–896 (2010).","allTopics":["systems-biology","ode","erbb-signaling-network","python"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":1,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2020-08-22T05:49:10.496Z"}},{"type":"Public","name":"Birtwistle2007","owner":"okadalabipr","isFork":false,"description":"Birtwistle, M. R. et al. Ligand-dependent responses of the ErbB signaling network: Experimental and modeling analyses. Mol. Syst. Biol. 3, (2007).","allTopics":["python","systems-biology","ode","julia","erbb-signaling-network"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":1,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2020-08-16T07:16:48.977Z"}},{"type":"Public","name":"Hatakeyama2003","owner":"okadalabipr","isFork":false,"description":"Hatakeyama, M. et al. A computational model on the modulation of mitogen-activated protein kinase (MAPK) and Akt pathways in heregulin-induced ErbB signalling. Biochem. J. 373, 451–463 (2003).","allTopics":["python","modeling","systems-biology","ode","erbb-signaling-network","matlab"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2020-08-05T10:04:37.525Z"}},{"type":"Public","name":"cancer_modeling","owner":"okadalabipr","isFork":false,"description":"Modeling signaling networks in cancer","allTopics":["modeling","systems-biology","computational-biology","ode","dde","reaction-network","differential-equations","cancer","signaling-pathways"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":3,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2020-07-20T00:40:59.158Z"}},{"type":"Public","name":"Michida2020","owner":"okadalabipr","isFork":false,"description":"Michida, H. et al. The number of transcription factors at an enhancer determines switch-like gene expression.","allTopics":["scrna-seq","chip-seq","atac-seq","enhancer"],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2020-06-30T09:01:30.890Z"}},{"type":"Public archive","name":"sensitivity_analysis","owner":"okadalabipr","isFork":false,"description":"Calculation of sensitivity coefficients and visualization","allTopics":["python","systems-biology","robustness","sensitivity","sensitivity-analysis"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2020-06-29T02:03:19.167Z"}},{"type":"Public","name":"Shinohara2014","owner":"okadalabipr","isFork":false,"description":"Shinohara, H. et al. Positive feedback within a kinase signaling complex functions as a switch mechanism for NF-κB activation. Science (80-. ). 344, 760–764 (2014).","allTopics":["python","systems-biology","ode","nfkb-dynamics"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":1,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2020-06-21T05:50:48.500Z"}},{"type":"Public archive","name":"intro_to_param_estim","owner":"okadalabipr","isFork":false,"description":"Parameter estimation of ODE models describing biological processes","allTopics":["python","optimization","modeling","systems-biology","computational-biology","parameter-estimation","genetic-algorithm"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":10,"forksCount":1,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2020-06-19T01:48:21.406Z"}},{"type":"Public","name":"Chiang2020","owner":"okadalabipr","isFork":false,"description":"Chiang, S., Shinohara, H., Huang, J. H., Tsai, H. K. & Okada, M. Inferring the transcriptional regulatory mechanism of signal-dependent gene expression via an integrative computational approach. FEBS Lett. (2020).","allTopics":["c","transcription-factors","systems-biology","computational-biology","mrna","gene-regulatory-network"],"primaryLanguage":{"name":"C","color":"#555555"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"BSD 2-Clause \"Simplified\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2020-04-23T00:38:39.227Z"}},{"type":"Public archive","name":"py2jl","owner":"okadalabipr","isFork":false,"description":"Converting Python code to Julia for ODE model construction","allTopics":["python","converter","julia","ode","ordinary-differential-equations","biomass"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":1,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2020-04-01T07:22:17.425Z"}},{"type":"Public","name":"egf_signaling","owner":"okadalabipr","isFork":false,"description":"Computational modeling of the short term pattern of cellular responses to epidermal growth factor","allTopics":["matlab","modeling","systems-biology","computational-biology","ode-model"],"primaryLanguage":{"name":"MATLAB","color":"#e16737"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2020-01-12T04:49:09.608Z"}}],"repositoryCount":29,"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":"okadalabipr repositories"}