{"database":"Cell Collective","file_versions":[],"scores":{"citationCount":8033,"reanalysisCount":0,"viewCount":0,"searchCount":0},"additional":{"omics_type":["Models"],"submitter":["Bhanwar Lal Puniya"],"version_name":[""],"full_dataset_link":["https://cellcollective.org/#6678/cd4+-t-cell-differentiation"],"model_score":["226.8538"],"default_version":["1"],"ModelFormat":["SBML"],"submitter_affiliation":[""],"submitter_email":[""],"version_id":["1"],"repository":["Cell Collective"],"version_url":["https://cellcollective.org/#6678:1/cd4+-t-cell-differentiation"],"version_description":["CD4+ T cell differentiation."],"pubmed_abstract":["<h4>Background</h4>Despite decades of new discoveries in biomedical research, the overwhelming complexity of cells has been a significant barrier to a fundamental understanding of how cells work as a whole. As such, the holistic study of biochemical pathways requires computer modeling. Due to the complexity of cells, it is not feasible for one person or group to model the cell in its entirety.<h4>Results</h4>The Cell Collective is a platform that allows the world-wide scientific community to create these models collectively. Its interface enables users to build and use models without specifying any mathematical equations or computer code - addressing one of the major hurdles with computational research. In addition, this platform allows scientists to simulate and analyze the models in real-time on the web, including the ability to simulate loss/gain of function and test what-if scenarios in real time.<h4>Conclusions</h4>The Cell Collective is a web-based platform that enables laboratory scientists from across the globe to collaboratively build large-scale models of various biological processes, and simulate/analyze them in real time. In this manuscript, we show examples of its application to a large-scale model of signal transduction."],"pubmed_title":["The Cell Collective: toward an open and collaborative approach to systems biology."],"pubmed_authors":["Helikar Tomáš T, Kowal Bryan B, McClenathan Sean S, Bruckner Mitchell M, Rowley Thaine T, Madrahimov Alex A, Wicks Ben B, Shrestha Manish M, Limbu Kahani K, Rogers Jim A JA"],"description_synonyms":["Thymus-Dependent Lymphocytes, Plays, Thing-1, SD-stat, induced regulatory T-lymphocyte, dstat, Dstat92E, Helix-loop-helix transcription factor expressed in extraembryonic mesoderm and trophoblast, dSTAT, jal, Gene, T-Lymphocyte, protein, xgata-3, protein-containing complex, Transcription Factor, Th1, HDRS, Th2, protrusion, DSRC, Responder protein Smok-Tcr, C77797, T Lymphocyte, Roles, T-bet, FOXP3, Gene Products, Concepts, Impacts, Environmental Impacts, IPEX, dSTAT92E, protein aggregate, immature T cell, XPID, TH1, Toy, RGD1562112, T-lymphocyte differentiation, Extraembryonic tissues, Transcription, Hxt, iTreg, mrL, Playthings, T-Cells, DmSTAT, GATA-3, JM2, ligand, CG4257, bHLHa26, sf, Stat, T, bHLHa27, NELF, d-STAT, induced regulatory T lymphocyte, Dstat 92E, AIID, Thing1, stat, Environmental Impact, T Cells, DmelCG9984, Thing2, mrl, Puppets, PIDX, TBT1, Dstat, mature T cell, Role Concepts, T cell development, dHAND, Play, STAT, stat92e, Gata-3, T Lymphocytes, Thymus Dependent Lymphocytes, Lymphocyte, DSTAT, l(3)06346, Puppet, single organism signaling, l(3)j6C8, induced regulatory T cell, AI661148, D-stat, Ligand, anatomical protrusion, TH1L, stat[92E], TBLYM, protein complex, T-lymphocyte receptor complex, DIETER, DRODSRC, Proteins, stat92E, pSTAT, Factor, D-STAT, Tbet, Cell, stat92, Impact, Concept, Environmental, 2.7.11.1, STAT 92E, Cytokine, Role Concept, TCR complex, T-Cell, Playthings and Play, heart, Protein, Role, Plaything, T lymphocyte differentiation, T-PET, T-cell differentiation., TBET, T lymphocyte, mrl stat92E, adaptive Treg, T lymphocyte receptor complex, Stat92, dSTAT92E/marelle, TCR, Tcr, T-cell, induced Treg, XGATA3, Factors, Th1l, STAT92E, Thymus-Dependent, Toys, Lymphocytes, CG9984, HDR, Ehand1, T-lymphocyte, Ehand2, Stat1alpha-like, Thymus-Dependent Lymphocyte, D-stat/stat92E, SmokTcr, aTreg, Protein Gene Products, NELF-D, Gene Proteins, extracellular, eHAND, T cell, Hed, DmelCG4257, signalling process, spine, 2410003I03Rik, AI225906, Cells, NELF-C, autonomic nervous system and neural crest derivatives-expressed protein 1, Environments, Dominant negative form of Smok, T Cell, T-cell receptor complex, D-Stat, induced regulatory T-cell, scurfin, Tblym"],"pubmed_title_synonyms":["Taf[[II]]250, Taf200, dTAF[[II]]230, TAF[[II]]250, d230, dTAF[[II]]250, TAF[[II]]230, TFIID TAF250, Collective, Systems., Biology, cel, cell, TAF200, l(3)84Ab, dTAFII250, Taf1p, TAF[II]250, BG:DS00004.13, TAFII-250, CG17603, TAF250/230, TAF[[II]], EfW1, Cell, dTAF230, dTAF250, dmTAF[[II]]230, TAFII250, DmelCG17603, Taf250, dmTAF1, SR3-5, Taf230, p230, TAF[[II]]250/230, TFIID, TAF, TAF230, TAF250, TAF1"],"name_synonyms":["Ly-4, T cell development, T-lymphocyte differentiation, T lymphocyte differentiation, CD4, T-cell differentiation., L3T4, CD4mut, T-cell surface antigen T4/Leu-3, T-cell surface antigen T4|Leu-3, T-cell differentiation antigen L3T4, T-cell surface glycoprotein CD4"],"pubmed_abstract_synonyms":["biochemical pathways, scale tissue, Signal Transductions, Activity, Laboratory, Mbp1, sci, Long Term, Calculators, dmTAF[[II]]230, Receptor Mediated Signal Transduction, Readability, eye, HOW, How, globe, Research Activity, Cell Signaling, myd, Laboratory Research, Effect, l(3)j5D5, 24B, Priorities, signal transduction by protein phosphorylation, TFIID TAF250, cel, catabolism, plant peltate hair, stru, Mbp-1, Pathways, l(3)S053606, CG10293, l(3)j5B5, set, Medicine, biotransformation, Signal Transduction Pathways, Transductions, Research Priority, Long-Term Effects, eye globe, 0904/17, 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TAF1"],"citation_count":["8033"],"additional_accession":[]},"is_claimable":false,"name":"CD4+ T cell Differentiation","description":"The model includes 38 components and 96 biochemical interactions that regulate the differentiation process of major T cell subtypes, i.e., Th1, Th2, Th17 and iTreg cells. Individual components of the model represent lineage-specifying transcription factors (Tbet, GATA3, RORt, and Foxp3), STAT proteins, cytokines, their receptors, and other signaling molecules. The extracellular environment is represented in the model by eight cytokines and a (generic) TCR ligand known to play a role in T cell differentiation. PMID: 22871178","dates":{"created":"2017-02-16","publication":"","submission":"2018-04-12","last_modified":"2018-04-12"},"accession":"6678","cross_references":{"pubmed":["22871178"]}}