http://www.inoh.org/inohblog/main/ Integrating Network Objects with Hierarchies en Copyright 2008 Mon, 04 Feb 2008 18:48:46 +0900 http://www.sixapart.com/movabletype/?v=3.2-ja-2 http://blogs.law.harvard.edu/tech/rss INOH client 2.0.2 does not officially support Mac OSX because some of its features require Java 6, which has not been made available from Apple yet. But if you only do browsing then you can use the linux version on your mac. See detailes in the "more" section bellow. http://www.inoh.org/inohblog/main/2008/02/inoh_client_mac_osx_support.html http://www.inoh.org/inohblog/main/2008/02/inoh_client_mac_osx_support.html Software Mon, 04 Feb 2008 18:48:46 +0900 here. This version is a major update and the version number is updated from 1.0.6 to 2.0.2. ===IMPORTANT!!!=== delete the "frame.layout" file in the .inoh directory of your home (e.g. Windows:C:\Documents and Settings\user-name,Linux:/home/user-name) before installing version 2.x. If not, panel pane will not appear correctly in your client. ]]> http://www.inoh.org/inohblog/main/2007/12/inoh_client_application_new_ve.html http://www.inoh.org/inohblog/main/2007/12/inoh_client_application_new_ve.html Mon, 03 Dec 2007 17:22:21 +0900 site. ====================== newly curated pathways ====================== EPO signaling pathway(JAK2 STAT1 STAT3 STAT5) Fas signaling pathway GPCR Adenosine A2A receptor signaling pathway TNFR1 signaling pathway ================= updated pathways ================= BMP2 signaling(through TAK1) BMP2 signaling(TGF-beta_signaling MolecularVariation) B cell receptor signaling CD4 T cell receptor signaling (JNK cascade) CD4 T cell receptor signaling (NF-kB cascade) CD4 T cell receptor signaling Drosophila IMD pathway Drosophila Toll-like receptor signaling EGF signaling pathway FGF signaling pathway GPCR Dopamine D1like receptor signaling pathway GPCR GroupI metabotropic glutamate receptor signaling pathway GPCR signaling (cholera toxin) GPCR signaling (G alpha i) GPCR signaling (G alpha q) GPCR signaling (G alpha s, Epac and ERK) GPCR signaling (G alpha s, PKA and ERK) GPCR signaling (pertussis toxin) Growth hormone signaling(JAK2 STAT5) HGF signaling pathway IFN gamma signaling(JAK1 JAK2 STAT1) IL-10 signaling(JAK1 TYK2 STAT3) Integrin signaling pathway JAK STAT MolecularVariation 1 JAK STAT MolecularVariation 2 JAK-STAT pathway and regulation pathway LIF signaling(JAK1 JAK2 STAT3) NGF signaling pathway TGF-beta signaling(through TAK1) TGF-beta_super_family_signaling_pathway(canonical) Toll-like receptor signaling pathway (through ECSIT, MEKK1, MKKs, JNK cascade) Toll-like receptor signaling pathway (through ECSIT, MEKK1, MKKs, p38 cascade) Toll-like receptor signaling pathway (through JNK cascade) Toll-like receptor signaling pathway (trough NF-kappaB) Toll-like receptor signaling pathway (p38 cascade) TPO signaling(JAK2 STAT3) VEGF signaling pathway C. elegans endoderm induction Wnt signaling pathway Diagram Canonical Wnt signaling pathway Diagram Drosophila Wingless/Wnt signaling pathway Diagram Mammalian Wnt signaling pathway Diagram Xenopus axis formation Wnt signaling pathway Diagram ]]> http://www.inoh.org/inohblog/main/2007/11/inoh_release_20_has_been_relea.html http://www.inoh.org/inohblog/main/2007/11/inoh_release_20_has_been_relea.html PathwayData Fri, 30 Nov 2007 16:07:44 +0900 BioPAX sourceforge CVS. Paxtools is a Domain Object Model(DOM) for BioPAX, providing software tools such as editors, exporters, importers, visualization tools and analysis algorithms with an API for manipulating BioPAX models. The Paxtools core model is developed at CBIO, MSKCC and the persistency layer is developed by INOH database. #NOTE: Currently we only have a "dev" version in the CVS. [documents] Find out here how to set up your Paxtools with a backbone DBMS. The javadoc for the Paxtools Level2 persistency layer API is available here. You can also get the pdf file of the paxtools poster abstract at ISMB 2007 here.]]> http://www.inoh.org/inohblog/main/2007/10/paxtools_level2_persistency_la.html http://www.inoh.org/inohblog/main/2007/10/paxtools_level2_persistency_la.html Software Thu, 25 Oct 2007 10:47:52 +0900 OBO site and from our download page. Statistics ========== All entries 8821 Chemicals 592 Proteins 8228 Obsoletes 25 UniProt ACs 5572 GO IDs 344 InterPro ACs 32 KEGG COMPOUND IDs 587 PubMed IDs 99]]> http://www.inoh.org/inohblog/main/2007/10/moleculerole_ontology_ver222.html http://www.inoh.org/inohblog/main/2007/10/moleculerole_ontology_ver222.html OntologyData Wed, 03 Oct 2007 17:44:41 +0900 OBO site and from our download page. Statistics ========== All entries 2781 Obsoletes 37 definition 470 GO IDs 406 KEGG PATHWAY IDs 184 Reactome IDs 110 PSI-MI IDs 68]]> http://www.inoh.org/inohblog/main/2007/10/event_ontology_ver162.html http://www.inoh.org/inohblog/main/2007/10/event_ontology_ver162.html OntologyData Wed, 03 Oct 2007 17:33:51 +0900 download site. ========== Statistics ========== BioPAX Level2 instances: control 105 catalysis 451 conversion 133 biochemicalReaction 469 complexAssembly 688 transport 124 physicalEntityParticipant 2479 sequenceParticipant 5104 pathway 332 pathwayStep 1670 complex 1621 dna 143 protein 2606 rna 60 smallMolecule 126]]> http://www.inoh.org/inohblog/main/2007/03/inoh_release_15_has_been_relea.html http://www.inoh.org/inohblog/main/2007/03/inoh_release_15_has_been_relea.html PathwayData Sat, 31 Mar 2007 11:47:45 +0900 OBO site and from our download page. Statistics ========== All entries 8649 Chemicals 592 Proteins 8056 Obsoletes 25 UniProt ACs 5465 GO IDs 329 InterPro ACs 32 KEGG COMPOUND IDs 587 PubMed IDs 81]]> http://www.inoh.org/inohblog/main/2007/03/moleculerole_ontology_ver221.html http://www.inoh.org/inohblog/main/2007/03/moleculerole_ontology_ver221.html OntologyData Thu, 29 Mar 2007 11:35:39 +0900 OBO site and from our download page. Statistics ========== All entries 2723 Obsoletes 21 definition 455 GO IDs 400 KEGG PATHWAY IDs 184 Reactome IDs 110 PSI-MI IDs 53]]> http://www.inoh.org/inohblog/main/2007/03/event_ontology_ver161.html http://www.inoh.org/inohblog/main/2007/03/event_ontology_ver161.html OntologyData Wed, 28 Mar 2007 19:11:36 +0900 INOH will be down from Feb 3 to Feb 5. Our host server at the Human Genome Center (HGC) will be shutdown due to scheduled system maintenance. ------------------------------------------------------------------------- NOTICE Due to the system maintenance and the electricity supply facilities maintenance , we will turn down all Supercomputers at HGC Until the maintenance of Supercomputers is completed, you will be unable to login the Supercomputers nor to use Web service during the following period: February 3, 2007 9:00 - February 5, 2007 9:00 The e-mail service will be stopped the following period: February 3, 2007 12:30 - February 3, 2007 17:00 The e-mail service will be temporarily suspended for 10-15min during 5-10pm. Sorry for any inconveniences that it may cause. System Administrator Super Computer System Human Genome Center http://www.inoh.org/inohblog/main/2007/01/system_maintenance_feb_3_900_a.html http://www.inoh.org/inohblog/main/2007/01/system_maintenance_feb_3_900_a.html Information Tue, 23 Jan 2007 14:56:00 +0900 OBO site and from our download page. Statistics ========== All entries 8457 Chemicals 592 Proteins 7864 Obsoletes 23 UniProt ACs 5286 GO IDs 322 InterPro ACs 32 KEGG COMPOUND IDs 587 PubMed IDs 78]]> http://www.inoh.org/inohblog/main/2006/11/moleculerole_ontology_ver220.html http://www.inoh.org/inohblog/main/2006/11/moleculerole_ontology_ver220.html OntologyData Wed, 01 Nov 2006 16:59:44 +0900 here. The update includes data error correction and new XREFs to various resources such as UniProt, IPR, KEGG, Reactome, GO, ChEBI.]]> http://www.inoh.org/inohblog/main/2006/09/inoh_biopax_level2_release_upd.html http://www.inoh.org/inohblog/main/2006/09/inoh_biopax_level2_release_upd.html PathwayData Thu, 28 Sep 2006 22:02:04 +0900 The latest Event Ontology is Ver.1.60 Event Ontology is an ontology of pathways. It classifies pathways, sub-pathways and other biological phenomena to form a DAG structure. You can download it from the OBO site and from our download page. http://www.inoh.org/inohblog/main/2006/08/event_ontology_ver160_1.html http://www.inoh.org/inohblog/main/2006/08/event_ontology_ver160_1.html OntologyData Wed, 23 Aug 2006 10:19:37 +0900 Download page and get each file separately or as a single archive. ]]> http://www.inoh.org/inohblog/main/2006/08/inoh_biopax_level2_release.html http://www.inoh.org/inohblog/main/2006/08/inoh_biopax_level2_release.html PathwayData Thu, 10 Aug 2006 17:12:55 +0900 User's manual Download Release Notes ====================== Version 1.0.6 bug fixes in "Type" edit slot of "SequenceFeature" Version 1.0.5 mouse-wheel support: Scroll Wheel - Pan vertically Ctrl+Scroll Wheel - Zoom ]]> http://www.inoh.org/inohblog/main/2006/05/inoh_client_ver106.html http://www.inoh.org/inohblog/main/2006/05/inoh_client_ver106.html Software Fri, 12 May 2006 16:35:20 +0900