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2011”N11ŒŽ14“ú
ƒTƒCƒg‚̈Ús‚ðŠJŽn‚µ‚Ü‚µ‚½
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http://cytoscape.wordpress.com/
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ƒTƒCƒgŠÇ—l Kieichiro Ono
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2011”N01ŒŽ27“ú
2/7/2011 “Œ‹ž‚Å‚ÌCytoscape Q&AƒZƒbƒVƒ‡ƒ“
‹}‚Å‚·‚ªAƒiƒ‰ƒvƒƒeƒNƒmƒƒW[ƒY—l(http://nalapro.com/)‚Ì‚²DˆÓ‚É‚æ‚èA‚Q^‚ViŒŽ—j“új‚É�ｿｽ�ｿｽ‹K–͂ȃ~[ƒeƒBƒ“ƒO‚ðŠJµ‚Ä‚�ｿｽ�ｿｽ‚½‚¾‚¯‚鎖‚É‚È‚è‚Ü‚µ‚½B
¡‰ñ‚ÍAŠù‚ÉCytoscape‚ðŽg‚Á‚Ä‚�ｿｽN‚ç‚ê‚é•û‚ւ̃vƒƒWƒFƒNƒg‚ÌŒ»óà–¾iCytoscape 2.x, Cytoscape 3, Cytoscape Web‚àŠÜ‚ÞjAQ&A‚È‚Ç‚É‚È‚é‚ÆŽv‚�ｿｽ�ｿｽ‚Ü‚·B
ŽÀÛ‚ÉŽg‚Á‚Ä‚�ｿｽN‚ç‚ê‚ÄA–â‘è‚È‚Ç‚ª‚ ‚éꇂÍA\”ñ‚�ｿｽ}‚Ì‹@‰ï‚É‚Ç‚¤‚¼B
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Cytoscape Core Developer
NRNB ( http://nrnb.org/ )
NRNB ( http://nrnb.org/ )
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Cytoscape‚Ì‘å–삳‚ñ‚ðŒ}‚¦‚ÄACytoscape‚ÉŠÖ‚·‚éQ & A ƒZƒbƒVƒ‡ƒ“‚ðŠJ·‚鎖‚É‚È‚è‚Ü‚µ‚½B‚²‹»–¡‚Ì‚ ‚é•û‚͉º‹L‚Ü‚Å\‚µž‚ÝA‚�ｿｽN–â‚�ｿｽ�ｿｽ‡‚킹‚‚¾‚³‚�ｿｽ�ｿｽB
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i“Œ‹ž“s•�ｿｽ�ｿｽ‹ž‹æ–{‹½2-40-17@–{‹½Žáˆäƒrƒ‹6F-Bj
info—nalapro.com
03-3813-6140
“úŽžF2ŒŽ7“úiŒŽj10Žž`12Žž
’èˆõFæ’…5–¼
êŠE\‚µž‚ÝæFƒiƒ‰ƒvƒEƒeƒNƒmƒƒW[ƒYŠ”Ž®‰ïŽÐ
i“Œ‹ž“s•�ｿｽ�ｿｽ‹ž‹æ–{‹½2-40-17@–{‹½Žáˆäƒrƒ‹6F-Bj
info—nalapro.com
03-3813-6140
“úŽžF2ŒŽ7“úiŒŽj10Žž`12Žž
’èˆõFæ’…5–¼
ƒ‰ƒxƒ‹Fcytoscape
2010”N06ŒŽ28“ú
Perl‚©‚çCytoscape‚ð—˜—p‚·‚é
CytoscapeRPC‚ÆŒ¾‚¤ƒvƒ‰ƒOƒCƒ“‚ª‚ ‚è‚Ü‚·‚ªA‚�ｿｽ}‚ê‚ð—˜—p‚·‚é‚�ｿｽ}‚Æ‚É‚æ‚èPerlƒXƒNƒŠƒvƒg‚©‚çCytoscape‚ð‘€ì‚·‚é‚�ｿｽ}‚Æ‚ª‚Å‚«‚Ü‚·B
ŠÈ’P‚È‚Í‚�ｿｽ�ｿｽ‚ß•û
“ÆŽ©ƒrƒ‹ƒh”ÅiˆË‘�ｿｽ�ｿｽŠÖŒW‚àˆê‚ɃpƒbƒN‚µ‚Ä‚ ‚è‚Ü‚·j‚ðƒ_ƒEƒ“ƒ[ƒh‚µ‚ÄpluginsƒtƒHƒ‹ƒ_‚ɃRƒs[‚·‚é
cytoscapeRPC.jar
Cytoscape‚ð‹N“®‚µAPluginƒƒjƒ…[‚©‚çCytoscapeRPC-->Activate Cytoscape RPC‚ð‘I‘ð‚·‚éBƒ|[ƒg”Ô†‚Í‚»‚Ì‚Ü‚Ü‚Å\‚�ｿｽ�ｿｽ‚Ü‚¹‚ñB
ƒXƒNƒŠƒvƒg‚ðŽÀs‚·‚é‘O‚ÉA—\‚ßCPAN‚©‚çFrontier::RPC2‚ðƒCƒ“ƒXƒg[ƒ‹‚µ‚Ä‚‚¾‚³‚�ｿｽ�ｿｽB
‚�ｿｽ}‚Ìó‘Ô‚Å—lX‚ȃƒ\ƒbƒh‚ðPerl‚©‚çŒÄ‚Ño‚·‚�ｿｽ}‚Æ‚ª‚Å‚«‚Ü‚·BƒTƒ“ƒvƒ‹ƒR[ƒh‚Í‚�ｿｽ}‚¿‚ç‚É‚ ‚è‚Ü‚·‚Ì‚ÅAFXC³‚µ‚È‚ª‚玎‚µ‚Ä‚Ý‚Ä‚‚¾‚³‚�ｿｽ�ｿｽ
https://wiki.nbic.nl/index.php/CytoscapeRPCPerlExample
2010”N04ŒŽ08“ú
Cytoscape 2.7‚ªƒŠƒŠ[ƒX‚³‚ê‚Ü‚µ‚½
‚�ｿｽN‘Ò‚½‚¹‚�ｿｽ�ｿｽ‚½‚µ‚Ü‚µ‚½BCytoscape‚ÌÅV”Å‚Å‚ ‚éƒo[ƒWƒ‡ƒ“2.7‚ªƒŠƒŠ[ƒX‚³‚ê‚Ü‚µ‚½Bæ‚É‚�ｿｽN’m‚点‚µ‚½V‹@”\’ljÁˆÈŠO‚É‚àA‚½‚‚³‚ñ‚̃oƒOC³‚ðŠÜ‚ñ‚Å‚�ｿｽN‚è‚Ü‚·‚Ì‚ÅA‚º‚ЃAƒbƒvƒf[ƒg‚µ‚Ä‚Ý‚Ä‚‚¾‚³‚�ｿｽ�ｿｽB
•s‹ï‡‚È‚Ç‚ ‚è‚Ü‚µ‚½‚çA“ú–{Œê‚̃[ƒŠƒ“ƒOƒŠƒXƒg‚©AŽ„‚Ì•û‚Ö’¼Ú‚Ç‚¤‚¼B
The Cytoscape team is proud to announce the release of Cytoscape 2.7! This
release includes some exciting new features:
* Nested Networks: A node may now have a reference to another Network,
which allows us to capture the relationships between networks in networks
themselves.
* CyCommandHandlers: Addition of a mechanism to the core to provide
inter-plugin communication.
* New Edge Types: Several new edge types between solid and dashed have been
added.
* Newlines and list editing in attribute browser: The attribute browser has
been updated to allow newline characters to be added by pressing the "Enter"
key. List editing is now also enabled.
* Automatic label wrap: A new visual property has been added that sets the
width of a label. Any label extending beyond this width will be
automatically wrapped.
* Arrow color optionally locked to edge color: Arrow color may now be bound
to the edge color by checking a box in the Dependencies pane of the Default
Appearance Browser in the VizMapper, which avoids the necessity of creating
separate-yet-identical mappings for edge, source, and target arrows.
* BioPAX Level 3 support.
You can get the release here: http://cytoscape.org
release includes some exciting new features:
* Nested Networks: A node may now have a reference to another Network,
which allows us to capture the relationships between networks in networks
themselves.
* CyCommandHandlers: Addition of a mechanism to the core to provide
inter-plugin communication.
* New Edge Types: Several new edge types between solid and dashed have been
added.
* Newlines and list editing in attribute browser: The attribute browser has
been updated to allow newline characters to be added by pressing the "Enter"
key. List editing is now also enabled.
* Automatic label wrap: A new visual property has been added that sets the
width of a label. Any label extending beyond this width will be
automatically wrapped.
* Arrow color optionally locked to edge color: Arrow color may now be bound
to the edge color by checking a box in the Dependencies pane of the Default
Appearance Browser in the VizMapper, which avoids the necessity of creating
separate-yet-identical mappings for edge, source, and target arrows.
* BioPAX Level 3 support.
You can get the release here: http://cytoscape.org
ƒ‰ƒxƒ‹Fcytoscape bioinformatics
2010”N03ŒŽ25“ú
Cytoscape‚ð—˜—p‚µ‚½˜_•�ｿｽ�ｿｽ‚Ì—á
Cytoscape‚ðŽg‚Á‚Ä‚Ý‚½‚�ｿｽ�ｿｽ‚ªA‚ǂ̂悤‚È—˜—p—Ⴊ‚ ‚é‚©H‚ÆŒ¾‚¤Ž¿–â‚ð‚µ‚Î‚µ‚Ύ󂯂é‚Ì‚Å‚·‚ªA˜_•�ｿｽ�ｿｽ‚Ì’†‚É‚ÍCytoscape‚ÌŽ–‚ðˆø—p‚µ‚Ä‚ ‚Á‚½‚肵‚Ä‚È‚©‚Á‚½‚è‚ÅAŽáŠ�ｿｽ}PubMed“™‚ÅŒŸõ‚µ‚É‚‚�ｿｽ�ｿｽ‚à‚Ì‚à‚ ‚è‚Ü‚·B—˜—p—á‚Æ‚µ‚ÄAŋ߂̘_•�ｿｽ�ｿｽ‚ð‚µ‚¾‚¯‚ ‚�ｿｽ�ｿｽ‚Ä‚Ý‚Ü‚·B
ˆÈ‰º‚̘_•�ｿｽ�ｿｽ‚ÍAƒiƒ‰ƒvƒƒeƒNƒmƒƒW[ƒYŽÐ‚̃eƒLƒXƒgƒ}ƒCƒjƒ“ƒO‹Zp‚ÆCytoscape‚ð—˜—p‚µ‚½AÅ‹ß”•\‚³‚ꂽ“ú–{‚ÌŒ¤‹†ŽÒ‚É‚æ‚é˜_•�ｿｽ�ｿｽ‚Ì—á‚Å‚·B
IQGAP1 and vimentin are key regulator genes in naturally occurring
hepatotumorigenesis induced by oxidative stress.
Tsubota A, Matsumoto K, Mogushi K, Nariai K, Namiki Y, Hoshina S, Hano
H, Tanaka H, Saito H, Tada N.
A preliminary approach to creating an overview of lactoferrin
multi-functionality utilizing a text mining method.
Shimazaki KI, Kushida T.
CytoscapeŠJ”‚ÉŠÖ‚í‚Á‚Ä‚�ｿｽ�ｿｽ‚éƒ`[ƒ€‚ªÅ‹ßo‚µ‚½˜_•�ｿｽ�ｿｽ‚Å‚àAƒlƒbƒgƒ[ƒN‚̉Ž‹‰»‚ƃf[ƒ^“‡•”•ª‚Å‚ÍA‚Ù‚Ú‚·‚�ｿｽ~‚ÄCytoscape‚ð—˜—p‚µ‚Ä‚�ｿｽ�ｿｽ‚Ü‚·‚Ì‚ÅAŽQl‚É‚µ‚Ä‚Ý‚Ä‚‚¾‚³‚�ｿｽ�ｿｽB
The genetic landscape of a cellScience. 2010 Jan 22;327(5964):425-31.
Genome Res. 2010 Feb;20(2):190-200. Epub 2009 Dec 9.
Bayesian network analysis of targeting interactions in chromatin.
PLoS Genet. 2009 Dec;5(12):e1000782. Epub 2009 Dec 24.
Genome-wide association data reveal a global map of genetic interactions among protein complexes.
Nature. 2010 Feb 11;463(7282):813-7.
Human host factors required for influenza virus replication.
ƒ‰ƒxƒ‹Fcytoscape
