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Folks The following issues were raised which were not covered by the existing model composition proposal on the SBML wiki (despite the tone of the language I'm actually ...
KimMorris 2010 07 22 Lock on door from writeup area to corner breakroom is installed backwards. It locks one out from break room in writeup area.
under construction... VCDB Curation Putting public models from VCDB into BMDB... List of public VC models to be curated/submitted to BMDB Model BioModel ...
Below are lines that can be added to the bottom of BNGL file to customize its SBML output for multicompartment representation. Please note that it works in alpha version ...
BioPAX (Biological Pathway Exchange) is an RDF based format to represent biological (meaning, usually biochemical, cellular) pathways. homepage OliverRuebenacker ...
CCAM's list of known problems and/or unsatisfied requirements at 400 Farmington Ave: Priorities Priority 1 Critical Priority 2 Important and urgent ...
Call for a workshop June 13th meeting at Santa Fe was successful in some ways (getting people together and getting them to agree that an SBML extension is a good ...
The following is a brief template of what should go into a proposal for this SBML L3 core enhancement. Goals and scope Use cases Syntax Description StefanHoops ...
Proposal The overall conclusion of the workshop was that 2 separate proposals will be developed. One will focus on the language elements required for the actual ...
Charles and Arlene Grossman Auditorium (Room 1210) AMX controls Controller web interface: http://ft amx ctrl 1210.cam.uchc.edu/ Note: this controller has ...
Room Fixed Priority Description Comments Ion comments Auditorium 1210
MartinGinkel 10 Sep 2007 From Ranjits Presentation: Models are composed from submodels, which are designed to be composed. This is, what is done in the Jigcell aggregation ...
Conference call 4/23/2008 Attendees : Ion, Harish, Jim, Anu. Topic : MIRIAM/Parameter annotations, etc. MIRIAM Annotations Presently, 'Add annotation' shows ...
GDB's, SCC's, and animal facility list of known problems and/or unsatisfied requirements at 400 Farmington Ave: Priorities Priority 1 Critical Priority ...
The following is a brief template of what should go into a proposal for this SBML L3 extension. It is written as an outline of the sections we envision being important ...
The following are unresolved issues and questions that arose from the first day of videoconferencing and post videoconference discussions at UCHC during the SBML Composition ...
2011 02 27 jlibSEDML 1.1.0 Release Notes jlibSEDML is intended to provide pure Java libraries to facilitate SED ML support for applications to: read, validate ...
JamesLi 2010 07 23 Locks need to be reprogramed so that only authorized personel can get in. Right now, everyone in the building can get in the facility.
1. General Goals (UseCase 1): Composing tool takes multiple traditional SBML models and creates composed model with minimal changes to the original ...
Actin Microfilaments Detector. Our task was to design and implement a software application able to process sets of images of biological structures within a cell, discriminate ...
Here I describe possible modifications of the core that would allow modularity and aggregation. IMHO, this is a prerequisite to any effort toward model composition ...
MartinGinkel 08 Sep 2007 Object Oriented Modeling in Promot Motivation Structured Models are very common in other simulation descriptions Examples: Simulink ...
General Rules Overloading involves the subtitution of a object and references to that object All objects are overloadable An object can't be overloaded ...
Object Type Overloadable Convergant Overloadable Divergant Overloadable Semantics Comments species yes no no flattened species ...
AnuradhaLakshminarayana 2009 08 25 In order for SBML to support spatial modeling, space must be considered explicitly. SBML describes molecular species and biochemical ...
The following is a brief template of what should go into a proposal for this SBML L3 extension. It is written as an outline of the sections we envision being important ...
Table of SBML language features and which tools support them Tool Algebraic Rules Rate Rules Assigment Rules Events Delay Time Function ...
SBPAX (pronounce: SY Bee Pucks) is short for Systems Biology Pathway Exchange. It is an RDF/OWL schema serving as a glue to integrate SBML/VCML type models with BioPAX ...
Introducing SBPAX #8211; A New Glue to Integrate SBML/VCML type Models with BioPAX type Pathways Computational biology has two thriving communities each with a large ...
Towards unifying systems biology using pathway data in BioPAX format for SBML simulators Thousands of biochemical interactions are available in the Biological Pathways ...
Towards unifying systems biology using pathway data in BioPAX format for SBML simulators Oliver Ruebenacker, Ion I. Moraru and Michael L. Blinov ...
Request for Support or Information Title: Adding an external membrane feature Question: I have a biomodel with two applications (deterministic and stochastic ...
Request for Support or Information Title: dendrite modeling Question: cut and paste from email VCell Version beta Computer OS Windows XP ...
The Virtual Cell SBML Converter VcmlSbmlConverter is a script used to convert SBML files to VCML and vice versa (import SBML files to VCML and export VCML files ...
Virtual Frap 1.0 screeshots Virtual Frap User Interface 1 Data Analysis Work Flow Wizard based work flow guides user through the whole process from loading ...
Useful Documents: Tips and Aides Parser.html: How to write expressions. Examples given in code syntax User Guide Hybrid ver2.pdf: Draft version of User Guide ...
AnuradhaLakshminarayana 2010 10 07 ICSB 2010 SBML Spatial Extension Attached are some snapshots of the XML schema for SBML Level 3 spatial extension and related ...
ICSB 2010 SBML Spatial Extension Snapshots of SBML L3 Spatial Extension package Previous efforts One of the SBML Level 3 Efforts is to add ways of representing the ...
AnuradhaLakshminarayana 2009 08 07 !!!! DISCLAIMER !!!! The summary of tools that support spatial modeling/geometries is a preliminary effort and may not be complete ...
TroubleShooting Post your question to our new Support Pages. Your questions and our answers will hopefully be useful to other users. These questions will be reviewed ...
Request for Support or Information Title: Question: VCell Version Computer OS Web browser Answer: Thank you for submitting a ...
SyBiL is short for Systems Biology Linker. It is a software currently able to load BioPAX data, analyze them and display them in a graph which can be customized in ...
Introducing SBPAX A New Glue to Integrate SBML/VCML type Models with BioPAX type Pathways Computational biology has two thriving communities each with a large pool ...
Frequently Asked and Troubleshooting Questions If your question is not addressed here, please send email to vcell support@uchc.edu. Include the version of Virtual ...
These pages are dedicated to user feedback and input. The developers of the Virtual Cell take seriously the needs of their users. These pages are one way users can ...
The way we do things Java syntactical conventions lexical rules for naming packages (categories) org.vcell is the beginning of each package all ...
Simulation Assisted Analysis of FRAP Experiments Introduction Flourescence Photobleaching Modern confocal microscopes provide the ability to perform ...
Virtual Microscopy Home JimSchaff 20 Aug 2008 AnnCowan 2010 09 09 tidbits to fix on VFRAP1.1 Load FRAP data wizard. Fix typo "varify/modify.." should be ...
The VCML Specification Version 0.4 Introduction The Virtual Cell Markup Language (VCML) is an XML document format for describing biological and mathematical models ...
JimSchaff 2010 09 15 VisIt integration Independent development projects Java viewerProxy integration of VCell client with VisIt Viewer component (Frank Morgan) ...
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SBML Level 3 Extensions Spatial Extension A page dedicated to the efforts to create an L3 extension for spatial modeling. Other SBML Extensions Focused SBML Workshops ...
IonMoraru RaquellHolmes .WebChangesAlert, ., .TWikiRegistration
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Topic revision: r5 - 2007-07-23 - 03:39:42 - IonMoraru
 
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