BioNetWiki - Recent changes [en]

Model Examples

2012-05-18T19:34:30Z

Revision as of 19:34, 18 May 2012		Current revision
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	**Role of talin, Dok1 and PIPKI in integrin activation		**Role of talin, Dok1 and PIPKI in integrin activation

		+
		+	[[Image: Dushek.png\|220px]]
	*<b>[http://www.cell.com/biophysj/abstract/S0006-3495(11)00145-7 Dushek, Merwe, Shahrezaei 2011]</b>		*<b>[http://www.cell.com/biophysj/abstract/S0006-3495(11)00145-7 Dushek, Merwe, Shahrezaei 2011]</b>
	** Multisite phosphorylation of membrane-anchored proteins		** Multisite phosphorylation of membrane-anchored proteins

		+
		+	[[Image: Chylek.png\|220px]]
	*<b>[http://www.ncbi.nlm.nih.gov/pubmed/21647530 Chylek, Blinov, Emonet, Faeder, Goldstein, Gutenkunst, Haugh, Lipniacki, Posner, Yang, Hlavacek 2011]</b>		*<b>[http://www.ncbi.nlm.nih.gov/pubmed/21647530 Chylek, Blinov, Emonet, Faeder, Goldstein, Gutenkunst, Haugh, Lipniacki, Posner, Yang, Hlavacek 2011]</b>
	**Extended contact map of early events in IgE receptor (FcεRI) signaling		**Extended contact map of early events in IgE receptor (FcεRI) signaling

		+	[[Image: Barua.png\|220px]]
	*<b>[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2667146/ Barua, Faeder, Haugh 2009]</b>		*<b>[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2667146/ Barua, Faeder, Haugh 2009]</b>
	**Activation of Jak-family protein tyrosine kinases		**Activation of Jak-family protein tyrosine kinases
		+
		+

	*<b>[http://www.ncbi.nlm.nih.gov/pubmed/20168997 Ray, Igoshin 2010]</b>		*<b>[http://www.ncbi.nlm.nih.gov/pubmed/20168997 Ray, Igoshin 2010]</b>

Special:Log/upload

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uploaded "[[Image:Chylek.png]]"

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uploaded "[[Image:Dushek.png]]"

Model Examples

2012-05-18T19:15:42Z

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Model Examples

2012-05-18T18:52:26Z

Revision as of 18:52, 18 May 2012

Current revision

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uploaded "[[Image:Kocieniewski.png]]"

Model Examples

2012-05-18T18:18:47Z

Revision as of 18:18, 18 May 2012		Current revision
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	*<b>[http://www.ncbi.nlm.nih.gov/pubmed/20168997 Ray, Igoshin 2010]</b>		*<b>[http://www.ncbi.nlm.nih.gov/pubmed/20168997 Ray, Igoshin 2010]</b>
		+	**Bacterial signaling through sensor histidine kinase and a transcriptional response regulator

	*<b>[http://www.ncbi.nlm.nih.gov/pubmed/21073233 Nag, Faeder, Goldstein]</b>		*<b>[http://www.ncbi.nlm.nih.gov/pubmed/21073233 Nag, Faeder, Goldstein]</b>
		+	**Role of FcεRI and Syk expression levels in mast cell signaling

	*<b>[http://papers.ssrn.com/sol3/papers.cfm?abstract_id=1666891 Kuhn, Hillmann 2010]</b>		*<b>[http://papers.ssrn.com/sol3/papers.cfm?abstract_id=1666891 Kuhn, Hillmann 2010]</b>
		+	**Labor market dynamics

	*<b>[http://www.ncbi.nlm.nih.gov/pubmed/21106117 Gong, Zuliani, Komuravelli, Faeder, Clarke 2010]</b>		*<b>[http://www.ncbi.nlm.nih.gov/pubmed/21106117 Gong, Zuliani, Komuravelli, Faeder, Clarke 2010]</b>
		+	**Overexpression of the High-mobility group box-1 (HMGB1) protein in the proliferation of various cancer types

	*<b>[http://www.nature.com/msb/journal/v6/n1/full/msb201090.html Feinerman, Jentsch, Tkach, et al. 2010]</b>		*<b>[http://www.nature.com/msb/journal/v6/n1/full/msb201090.html Feinerman, Jentsch, Tkach, et al. 2010]</b>
		+	**Interleukin-2 (IL-2) signaling in T cells

	*<b>[http://www.cell.com/biophysj/retrieve/pii/S0006349509004202 Nag, Monine, Faeder, et al. 2009]</b>		*<b>[http://www.cell.com/biophysj/retrieve/pii/S0006349509004202 Nag, Monine, Faeder, et al. 2009]</b>
		+	**Cross-linking of LAT in LAT-Grb2-SOS1 system

	*<b>[http://www.ncbi.nlm.nih.gov/pubmed/18835283 An, Faeder 2009]</b>		*<b>[http://www.ncbi.nlm.nih.gov/pubmed/18835283 An, Faeder 2009]</b>
		+	**TLR-4 signaling and preconditioning

	*<b>[http://www.springerlink.com/content/04v51u46144h1585/?MUD=MP Clarke, Faeder, Landmead et al. 2008]</b>		*<b>[http://www.springerlink.com/content/04v51u46144h1585/?MUD=MP Clarke, Faeder, Landmead et al. 2008]</b>
		+	**Verification of T-cell receptor signaling pathway model using <i>BioLab</i>

	*<b>[http://www.jbc.org/content/283/12/7338 Barua, Faeder, Haugh 2008]</b>		*<b>[http://www.jbc.org/content/283/12/7338 Barua, Faeder, Haugh 2008]</b>
		+	**Tandem Src Homology 2 Domain interactions and application to Phosphoinositide 3-Kinase

	*<b>[http://www.ncbi.nlm.nih.gov/pubmed/17933853 Mu, Williams, Unkefer, et al. 2007]</b>		*<b>[http://www.ncbi.nlm.nih.gov/pubmed/17933853 Mu, Williams, Unkefer, et al. 2007]</b>
		+	**Carbon-fate maps for metabolic reactions

	*<b>[http://www.cell.com/biophysj/retrieve/pii/S0006349507710366 Barua, Faeder Haugh 2007]</b>		*<b>[http://www.cell.com/biophysj/retrieve/pii/S0006349507710366 Barua, Faeder Haugh 2007]</b>
		+	**Shp2 in intracellular signal transduction

	*<b>[http://www.ncbi.nlm.nih.gov/pubmed/16233948 Blinov, Faeder, Goldstein, et al. 2006]</b>		*<b>[http://www.ncbi.nlm.nih.gov/pubmed/16233948 Blinov, Faeder, Goldstein, et al. 2006]</b>
		+	**Early events in signaling by the epidermal growth factor (EGF) receptor (EGFR)

	*<b>[http://www.ncbi.nlm.nih.gov/pubmed/17091578 Faeder, Blinov, Goldstein 2005]</b>		*<b>[http://www.ncbi.nlm.nih.gov/pubmed/17091578 Faeder, Blinov, Goldstein 2005]</b>
		+	**Signaling by the immunoreceptor FcεRI

	*<b>[http://www.ncbi.nlm.nih.gov/pubmed/12646643 Faeder Hlavacek Reischl et al. 2003]</b>		*<b>[http://www.ncbi.nlm.nih.gov/pubmed/12646643 Faeder Hlavacek Reischl et al. 2003]</b>
		+	**Early events in FcεRI-mediated signaling

	==Models in the BioNetGen Distribution==		==Models in the BioNetGen Distribution==

Main Page

2012-05-18T14:25:24Z

/* News */

Revision as of 14:25, 18 May 2012		Current revision
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	==News==		==News==
		+	* [http://www.biomedcentral.com/1471-2105/13/S8/S3 A full-length paper] describing [http://rulebender.org RuleBender], our graphical front-end for rule-based modeling, was just published in a BMC Bioinformatics Supplement [http://www.biomedcentral.com/bmcbioinformatics/supplements/13/S8 Highlights of the 1st IEEE Symposium on Biological Data Visualization (BioVis 2011)].
	* Join the new [https://groups.google.com/d/forum/bionetgen-users BioNetGen users'] google group to get all of the latest updates. It's also a great forum for asking questions and starting discussions.		* Join the new [https://groups.google.com/d/forum/bionetgen-users BioNetGen users'] google group to get all of the latest updates. It's also a great forum for asking questions and starting discussions.
	* BioNetGen (2.2.0-stable) is now available for [[BioNetGen_Distributions \| download]], featuring:		* BioNetGen (2.2.0-stable) is now available for [[BioNetGen_Distributions \| download]], featuring:

Model Examples

2012-05-18T00:25:13Z

Revision as of 00:25, 18 May 2012		Current revision
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	*[[Dimerization_cBNGL]]		*[[Dimerization_cBNGL]]
	*[[Enzymatic Cycle]]		*[[Enzymatic Cycle]]
-
-	==Models in the BioNetGen Distribution==
-
-	The source code for each model (BioNetGen language files with the .bngl extension) is included in the Models2 directory of the BioNetGen distribution.
-	*[[egfr_simple]]
-	*[[egfr_net]]
-	*[[egfr_path]]
-	*[[blbr]]
-	*[[fceri]]
-	*[[toy-jim]]
-	*[[SHP2_base_model]]

	==Models from Published Papers==		==Models from Published Papers==
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	*<b>[http://www.ncbi.nlm.nih.gov/pubmed/12646643 Faeder Hlavacek Reischl et al. 2003]</b>		*<b>[http://www.ncbi.nlm.nih.gov/pubmed/12646643 Faeder Hlavacek Reischl et al. 2003]</b>
		+
		+	==Models in the BioNetGen Distribution==
		+
		+	The source code for each model (BioNetGen language files with the .bngl extension) is included in the Models2 directory of the BioNetGen distribution.
		+	*[[egfr_simple]]
		+	*[[egfr_net]]
		+	*[[egfr_path]]
		+	*[[blbr]]
		+	*[[fceri]]
		+	*[[toy-jim]]
		+	*[[SHP2_base_model]]

	==Other Models==		==Other Models==

Main Page

2012-05-18T00:19:51Z

/* News */

Revision as of 00:19, 18 May 2012		Current revision
Line 4:		Line 4:

	==News==		==News==
		+	* Join the new [https://groups.google.com/d/forum/bionetgen-users BioNetGen users'] google group to get all of the latest updates. It's also a great forum for asking questions and starting discussions.
	* BioNetGen (2.2.0-stable) is now available for [[BioNetGen_Distributions \| download]], featuring:		* BioNetGen (2.2.0-stable) is now available for [[BioNetGen_Distributions \| download]], featuring:
	** Full support for ratelaws defined by functions of model observables.		** Full support for ratelaws defined by functions of model observables.

Model Examples

2012-05-17T19:45:02Z

Revision as of 19:45, 17 May 2012		Current revision
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	**Activation of Jak-family protein tyrosine kinases		**Activation of Jak-family protein tyrosine kinases

-	*[[Faeder2003]]	+	*<b>[http://www.ncbi.nlm.nih.gov/pubmed/20168997 Ray, Igoshin 2010]</b>
-	*[[Faeder2005]]	+
-	*[[Blinov2006]]	+	*<b>[http://www.ncbi.nlm.nih.gov/pubmed/21073233 Nag, Faeder, Goldstein]</b>
-	*[[Barua2007]]	+
-	*[[Barua2008]]	+	*<b>[http://papers.ssrn.com/sol3/papers.cfm?abstract_id=1666891 Kuhn, Hillmann 2010]</b>
-	*[[Borisov2008]]	+
-	*[[Lipniacki2008]]	+	*<b>[http://www.ncbi.nlm.nih.gov/pubmed/21106117 Gong, Zuliani, Komuravelli, Faeder, Clarke 2010]</b>
-	*[[Mu2008]]	+
-	*[[An2009]]	+	*<b>[http://www.nature.com/msb/journal/v6/n1/full/msb201090.html Feinerman, Jentsch, Tkach, et al. 2010]</b>
-	*[[Harris2009]]	+
-	*[[Nag2009]]	+	*<b>[http://www.cell.com/biophysj/retrieve/pii/S0006349509004202 Nag, Monine, Faeder, et al. 2009]</b>
-	*[[Monine2010]]	+
		+	*<b>[http://www.ncbi.nlm.nih.gov/pubmed/18835283 An, Faeder 2009]</b>
		+
		+	*<b>[http://www.springerlink.com/content/04v51u46144h1585/?MUD=MP Clarke, Faeder, Landmead et al. 2008]</b>
		+
		+	*<b>[http://www.jbc.org/content/283/12/7338 Barua, Faeder, Haugh 2008]</b>
		+
		+	*<b>[http://www.ncbi.nlm.nih.gov/pubmed/17933853 Mu, Williams, Unkefer, et al. 2007]</b>
		+
		+	*<b>[http://www.cell.com/biophysj/retrieve/pii/S0006349507710366 Barua, Faeder Haugh 2007]</b>
		+
		+	*<b>[http://www.ncbi.nlm.nih.gov/pubmed/16233948 Blinov, Faeder, Goldstein, et al. 2006]</b>
		+
		+	*<b>[http://www.ncbi.nlm.nih.gov/pubmed/17091578 Faeder, Blinov, Goldstein 2005]</b>
		+
		+	*<b>[http://www.ncbi.nlm.nih.gov/pubmed/12646643 Faeder Hlavacek Reischl et al. 2003]</b>

	==Other Models==		==Other Models==

Release Notes

2012-05-17T04:08:25Z

/* new actions */

Revision as of 04:08, 17 May 2012		Current revision
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	==== new actions ====		==== new actions ====

-	See the [[Documentation#The_BioNetGen_Syntax_Guide \| quick reference quide]] for complete and up-to-date documentation of BioNetGen actions, options and values. Actions new to version 2.2.0 are briefly described below:	+	See the [[Documentation#The_BioNetGen_Syntax_Guide \| quick syntax quide]] for complete and up-to-date documentation of BioNetGen actions, options and values. Actions new to version 2.2.0 are briefly described below:

-	<big><code>addConcentration("SPECIES","VALUE">)</code></big>	+	<big><code>addConcentration("SPECIES","VALUE")</code></big>
	* Add concentration to a species.		* Add concentration to a species.
	* SPECIES is a string specifying the species.		* SPECIES is a string specifying the species.
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	<big><code>saveParameters(["LABEL"])</code></big>		<big><code>saveParameters(["LABEL"])</code></big>
	* Save the current parameter values.		* Save the current parameter values.
-	* Optional LABEL argument assigns a label to the saved parameters.	+	* Optional LABEL argument assigns a label to the saved parameters. (Square braces indicate an optional argument.)

	<big><code>resetParameters(["LABEL"])</code></big>		<big><code>resetParameters(["LABEL"])</code></big>
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	* Rare parsing error in functions block forced BNG abort. Parsing error is alleviated (for unknown reason) if the optional "=" operator is placed between the function name and definition.		* Rare parsing error in functions block forced BNG abort. Parsing error is alleviated (for unknown reason) if the optional "=" operator is placed between the function name and definition.
	* Network-based simulations do not support molecule-scoped local functions. At present, this functionality is NFsim-only.		* Network-based simulations do not support molecule-scoped local functions. At present, this functionality is NFsim-only.
-	* Functions do not accept numerical arguments. At present, function arguments are limited to species and molecule tags (See NFsim manual, chapter 6, for full details. The NFsim manual can be obtained by registering for [http://emonet.biology.yale.edu/nfsim/ NFsim] and downloading the distribution	+	* Functions do not accept numerical arguments. At present, function arguments are limited to species and molecule tags (See NFsim manual, chapter 6, for full details. The NFsim manual can be obtained by registering for [http://emonet.biology.yale.edu/nfsim/ NFsim] and downloading the distribution.
		+	* BNG2.pl won't respect BNGPATH environment variable (fortunately BNG2 is pretty good about finding its own path).
		+	* Perl may issue "uninitialized value in numerical comparison" warning during network generation for rules combing molecule deletion and binding. This warning may be safely ignored.

	= BioNetGen 2.1 releases =		= BioNetGen 2.1 releases =

BioNetGen Distributions

2012-05-17T03:45:52Z

/* Source Code Distribution */

Revision as of 03:45, 17 May 2012		Current revision
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	** Full support for ratelaws defined as functions of models observables.		** Full support for ratelaws defined as functions of models observables.
	** Partitioned Leaping Algorithm (PLA) for accelerated stochastics.		** Partitioned Leaping Algorithm (PLA) for accelerated stochastics.
-	** See [[Release_Notes#version_2.2.0_stable \| revision notes]] for more details.	+	** See [[Release_Notes#version_2.2.0_stable \| release notes]] for more details.

	*'''Download the previous release [http://dl.dropbox.com/u/19644336/BioNetGen_2.1.8_rev597.tgz BioNetGen 2.1.8 revision 597]'''		*'''Download the previous release [http://dl.dropbox.com/u/19644336/BioNetGen_2.1.8_rev597.tgz BioNetGen 2.1.8 revision 597]'''

Special:Log/upload

2012-05-16T18:46:12Z

uploaded "[[Image:Tiger2012.png]]"

Special:Log/upload

2012-05-16T18:36:29Z

uploaded "[[Image:Tiger2012.png]]"

Model Examples

2012-05-16T18:31:33Z

Revision as of 18:31, 16 May 2012		Current revision
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	==Models from Published Papers==		==Models from Published Papers==
		+
		+	*<b>[http://www.nature.com/msb/journal/v8/n1/full/msb201212.html Tiger, Krause, Cedersun, Palmer, Klipp, Hohmann, Kitano, Krantz 2012]</b>
		+	**Comprehensive map of the yeast MAP kinase network
		+
		+	*<b>[http://www.ncbi.nlm.nih.gov/pubmed/22123371 Kocieniewski, Faeder, Lipniacki 2012]</b>
		+	**Double phosphorylation and scaffolding in MAP kinase pathways
		+
		+	*<b>[http://www.pnas.org/content/early/2011/11/22/1004042108.abstract Thomson, Benjamin, Bush, Love, Pincus, Resnekov, Yu, Gordon, Colman-Lerner, Endy, Brent 2011]</b>
		+	**Yeast pheromone response pathway
		+
		+	*<b>[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0024808 Geier, Fengos, Iber 2011]</b>
		+	**Role of talin, Dok1 and PIPKI in integrin activation
		+
		+	*<b>[http://www.cell.com/biophysj/abstract/S0006-3495(11)00145-7 Dushek, Merwe, Shahrezaei 2011]</b>
		+	** Multisite phosphorylation of membrane-anchored proteins
		+
		+	*<b>[http://www.ncbi.nlm.nih.gov/pubmed/21647530 Chylek, Blinov, Emonet, Faeder, Goldstein, Gutenkunst, Haugh, Lipniacki, Posner, Yang, Hlavacek 2011]</b>
		+	**Extended contact map of early events in IgE receptor (FcεRI) signaling
		+
		+	*<b>[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2667146/ Barua, Faeder, Haugh 2009]</b>
		+	**Activation of Jak-family protein tyrosine kinases

	*[[Faeder2003]]		*[[Faeder2003]]
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	*[[Mu2008]]		*[[Mu2008]]
	*[[An2009]]		*[[An2009]]
-	*[[Barua2009]]
	*[[Harris2009]]		*[[Harris2009]]
	*[[Nag2009]]		*[[Nag2009]]

Release Notes

2012-05-15T02:05:46Z

/* known issues */ point user to NFsim doumentation

Revision as of 02:05, 15 May 2012		Current revision
Line 5:		Line 5:

	==== pre-compiled binaries ====		==== pre-compiled binaries ====
		+	Included with the distribution:
	* GNU/Linux for x86 and x86_64 architectures		* GNU/Linux for x86 and x86_64 architectures
-	* Max OS/X for x86 architecture (compiled under 10.5/Leopard)	+	* Mac OS/X for x86 architecture (compiled under 10.5/Leopard)
	* Windows for x86 architecture (compiled in Cygwin environment and distributed with Cygwin DLL).		* Windows for x86 architecture (compiled in Cygwin environment and distributed with Cygwin DLL).
		+	Available for [[BioNetGen_Distributions#Precompiled_Binaries\|download]], but not part of distribution:
		+	* Mac OS/X for x86_64 (compiled under 10.7/Lion)

	==== run_network v3, stable release ====		==== run_network v3, stable release ====
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	==== new actions ====		==== new actions ====

-	(need link to actions document)	+	See the [[Documentation#The_BioNetGen_Syntax_Guide \| quick reference quide]] for complete and up-to-date documentation of BioNetGen actions, options and values. Actions new to version 2.2.0 are briefly described below:

	<big><code>addConcentration("SPECIES","VALUE">)</code></big>		<big><code>addConcentration("SPECIES","VALUE">)</code></big>
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	* Fixed species property is now respected in stochastic simulations (SSA,PLA) in all cases. Previously, the population of a fixed species could change in stochastic simulations if the species appeared as a reactant (but not a product) in a reaction.		* Fixed species property is now respected in stochastic simulations (SSA,PLA) in all cases. Previously, the population of a fixed species could change in stochastic simulations if the species appeared as a reactant (but not a product) in a reaction.
	* BNG will save and load models with relaxed typing (e.g. no molecule types block) without error. Previous versions wrote an incomplete molecule types bloc, leading to problems when the file was reloaded.		* BNG will save and load models with relaxed typing (e.g. no molecule types block) without error. Previous versions wrote an incomplete molecule types bloc, leading to problems when the file was reloaded.
		+	* Fixed ratelaw multiplier calculation: incorrect multiplier was calculated for rules with 2 or more identical reactant patterns that do not contain reaction center (i.e. not transformed by the reaction rule). Examples of affected rules:
		+	** synthesis reaction driven by symmetric interaction: <code>X + X -> X + X + Y k</code>
		+	** tri-molecular transformation with symmetric reactants and assymetric products: <code>X + X + X -> X + X + Y k</code>

	==== known issues ====		==== known issues ====
	* M-file script generated by <code>writeMfile</code> action will abort abruptly if MATLAB ode23s integrator fails but does not throw an exception(MATLAB issues warning instead of error).		* M-file script generated by <code>writeMfile</code> action will abort abruptly if MATLAB ode23s integrator fails but does not throw an exception(MATLAB issues warning instead of error).
	* Rare parsing error in functions block forced BNG abort. Parsing error is alleviated (for unknown reason) if the optional "=" operator is placed between the function name and definition.		* Rare parsing error in functions block forced BNG abort. Parsing error is alleviated (for unknown reason) if the optional "=" operator is placed between the function name and definition.
		+	* Network-based simulations do not support molecule-scoped local functions. At present, this functionality is NFsim-only.
		+	* Functions do not accept numerical arguments. At present, function arguments are limited to species and molecule tags (See NFsim manual, chapter 6, for full details. The NFsim manual can be obtained by registering for [http://emonet.biology.yale.edu/nfsim/ NFsim] and downloading the distribution

	= BioNetGen 2.1 releases =		= BioNetGen 2.1 releases =

-	== version 2.1.8 testing ==	+	== version 2.1.8 ==
-	This release appears to be stable, but is still considered a beta release. We welcome feedback and bug reports. Thanks.	+	This release is no longer in active development. Revision 597 was the last update.
		+
		+	=== Revision Notes: 597 (final 2.1.8 release) ===
		+
		+	* '''BUG NOTICE''' (fixed in 2.2.0): Incorrect ratelaw multiplier is calculated for rules with 2 or more identical reactant patterns that do not contain reaction center (i.e. not transformed by the reaction rule). Upgrade to 2.2+ is recommended if your model contains rules with higher-order reactions (molecularity>2). Examples of affected rules:
		+	** synthesis reaction driven by symmetric interaction: <code>X + X -> X + X + Y k</code>
		+	** tri-molecular transformation with symmetric reactants and assymetric products: <code>X + X + X -> X + X + Y k</code>
		+	* fixed bug that caused a fatal error when setParameter action is called with an unquoted parameter name.
		+	* fixed bug that, under certain conditions, resulted in failure to update .net file prior to simulation.
		+
		+	=== Revision Notes: 549 ===
		+
		+	* '''BUG NOTICE''' (fixed in 597): a fatal error is produced if the setParameter action is called with an unquoted parameter name. This error can be avoided by adding quotes to the parameter name. The parameter scanning script 'scan_var.pl' is affected by this bug. A quick fix is possible by commenting out the "use strict" pragma in Perl2/BNGModel.pm.
		+	* '''BUG NOTICE''' (fixed in rev597): under certain conditions the .net file is not updated prior to simulation. This occurs when an old .net file already exists with the same name and the UpdateNet flag is false. Deleting the old NET file will resolve the issue.
		+	**The main BioNetGen executable script 'BNG2.pl' has been relocated to the root directory. This may cause temporary incompatibility with RuleBender.
		+	*Output files are now written to the current working directory by default. Previously the default path was the directory containing the model. The default path may be changed by calling BNG2.pl with the argument '-outdir PATH'. Alternatively, passing the 'prefix' option to BNG actions will override default path and filename prefix.
		+	*Fixed a bug in writeSBML() that caused failure when writing derived parameters.
		+	*Fixed bug in Network3 simulator that caused failure of some SSA simulations with functional ratelaws.
		+	*Fixed a bug in handling rate multiplicities of symmetric reactions with multiple component tags (uncommon).
		+	*Minor improvements to output actions writeMfile() and writeMexfile() with regards to MATLAB plot asthetics and filename handling.
		+	*New test feature: BNGconsole. Execute 'BNG2.pl -console' to start a simple interactive console. This is a sandbox feature and is not yet fully developed.
		+	*Thanks to extensive user feedback, we have greatly expanded our set of validation models. This should improve reliability of future releases.

	==== New features ====		==== New features ====
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	* On-the-fly network generation is not supported in Network3 (please use Network2).		* On-the-fly network generation is not supported in Network3 (please use Network2).
	* Infinite loop encountered in Makefile if "clean" recipe is executed while subdirectories are missing (ctrl-c will terminate the loop).		* Infinite loop encountered in Makefile if "clean" recipe is executed while subdirectories are missing (ctrl-c will terminate the loop).
-
-	=== Revision Notes: 597 ===
-
-	* fixed bug that caused a fatal error when setParameter action is called with an unquoted parameter name.
-	* fixed bug that, under certain conditions, resulted in failure to update .net file prior to simulation.
-
-	=== Revision Notes: 549 ===
-
-	* ''BUG NOTICE'' (fixed in 597): a fatal error is produced if the setParameter action is called with an unquoted parameter name. This error can be avoided by adding quotes to the parameter name. The parameter scanning script 'scan_var.pl' is affected by this bug. A quick fix is possible by commenting out the "use strict" pragma in Perl2/BNGModel.pm.
-	* ''BUG NOTICE'' (fixed in rev597): under certain conditions the .net file is not updated prior to simulation. This occurs when an old .net file already exists with the same name and the UpdateNet flag is false. Deleting the old NET file will resolve the issue.
-	**The main BioNetGen executable script 'BNG2.pl' has been relocated to the root directory. This may cause temporary incompatibility with RuleBender.
-	*Output files are now written to the current working directory by default. Previously the default path was the directory containing the model. The default path may be changed by calling BNG2.pl with the argument '-outdir PATH'. Alternatively, passing the 'prefix' option to BNG actions will override default path and filename prefix.
-	*Fixed a bug in writeSBML() that caused failure when writing derived parameters.
-	*Fixed bug in Network3 simulator that caused failure of some SSA simulations with functional ratelaws.
-	*Fixed a bug in handling rate multiplicities of symmetric reactions with multiple component tags (uncommon).
-	*Minor improvements to output actions writeMfile() and writeMexfile() with regards to MATLAB plot asthetics and filename handling.
-	*New test feature: BNGconsole. Execute 'BNG2.pl -console' to start a simple interactive console. This is a sandbox feature and is not yet fully developed.
-	*Thanks to extensive user feedback, we have greatly expanded our set of validation models. This should improve reliability of future releases.

	== version 2.1.7 ==		== version 2.1.7 ==

Image:BNG syntax keywords.pdf

2012-05-11T19:13:31Z

Revision as of 19:13, 11 May 2012	Current revision
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-	+	This image can be deleted. The syntax guide is linked to in the [http://bionetgen.org/index.php/Documentation Documentation] page via a public dropbox URL instead.

Documentation

2012-05-11T19:02:20Z

/* Key Documents */

Revision as of 19:02, 11 May 2012		Current revision
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	The [http://dl.dropbox.com/u/9028382/Reprints/RuleBasedPrimer-2011.pdf Primer] provides a gentle introduction to rule-based modeling with BioNetGen.		The [http://dl.dropbox.com/u/9028382/Reprints/RuleBasedPrimer-2011.pdf Primer] provides a gentle introduction to rule-based modeling with BioNetGen.

-	===[http://dl.dropbox.com/u/7096948/BNG_syntax_keywords.pdf The BioNetGen Syntax Guide]===	+	===[http://dl.dropbox.com/u/13228396/BNG_syntax_keywords.pdf The BioNetGen Syntax Guide]===
-	The [http://dl.dropbox.com/u/7096948/BNG_syntax_keywords.pdf syntax guide] provides a list of the different symbols, keywords and actions used in BioNetGen, alongside with a short description. This is a handy reference for users familiar with the basics.	+	The [http://dl.dropbox.com/u/13228396/BNG_syntax_keywords.pdf syntax guide] provides a list of the different symbols, keywords and actions used in BioNetGen, alongside with a short description. This is a handy reference for users familiar with the basics.

	===[http://stke.sciencemag.org/cgi/content/full/sigtrans;2006/344/re6?ijkey=g7njdDmsvuHUw&keytype=ref&siteid=sigtrans Review of Rule-Based Modeling]===		===[http://stke.sciencemag.org/cgi/content/full/sigtrans;2006/344/re6?ijkey=g7njdDmsvuHUw&keytype=ref&siteid=sigtrans Review of Rule-Based Modeling]===

Special:Log/upload

2012-05-11T18:50:10Z

uploaded "[[Image:BNG syntax keywords.pdf]]"

Revision as of 19:15, 18 May 2012		Current revision
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	==Models from Published Papers==		==Models from Published Papers==

		+	[[Image: tiger2012.png\|100px]]
	*<b>[http://www.nature.com/msb/journal/v8/n1/full/msb201212.html Tiger, Krause, Cedersun, Palmer, Klipp, Hohmann, Kitano, Krantz 2012]</b>		*<b>[http://www.nature.com/msb/journal/v8/n1/full/msb201212.html Tiger, Krause, Cedersun, Palmer, Klipp, Hohmann, Kitano, Krantz 2012]</b>
	**Comprehensive map of the yeast MAP kinase network		**Comprehensive map of the yeast MAP kinase network

		+
		+	[[Image: kocieniewski.png\|220px]]
	*<b>[http://www.ncbi.nlm.nih.gov/pubmed/22123371 Kocieniewski, Faeder, Lipniacki 2012]</b>		*<b>[http://www.ncbi.nlm.nih.gov/pubmed/22123371 Kocieniewski, Faeder, Lipniacki 2012]</b>
	**Double phosphorylation and scaffolding in MAP kinase pathways		**Double phosphorylation and scaffolding in MAP kinase pathways

		+
		+	[[Image: thomson.png\|220px]]
	*<b>[http://www.pnas.org/content/early/2011/11/22/1004042108.abstract Thomson, Benjamin, Bush, Love, Pincus, Resnekov, Yu, Gordon, Colman-Lerner, Endy, Brent 2011]</b>		*<b>[http://www.pnas.org/content/early/2011/11/22/1004042108.abstract Thomson, Benjamin, Bush, Love, Pincus, Resnekov, Yu, Gordon, Colman-Lerner, Endy, Brent 2011]</b>
	**Yeast pheromone response pathway		**Yeast pheromone response pathway

		+
		+	[[Image: geier.png\|220px]]
	*<b>[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0024808 Geier, Fengos, Iber 2011]</b>		*<b>[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0024808 Geier, Fengos, Iber 2011]</b>
	**Role of talin, Dok1 and PIPKI in integrin activation		**Role of talin, Dok1 and PIPKI in integrin activation