This is list of people who have registered to attend this years Hackathon (a total of 34 people).
Researchers in quantitative systems biology make use of a large number of different software packages for modeling, analysis, visualization, and general data manipulation. The Systems Biology Workbench (SBW), is a software framework that allows heterogeneous application components-written in diverse programming languages and running on different platforms - to communicate and use each others' capabilities via a fast binary encoded-message system. Our goal was to create a simple, high performance, open-source software infrastructure which is easy to implement and understand. SBW enables applications (potentially running on separate, distributed computers) to communicate via a simple network protocol. The interfaces to the system are encapsulated in client-side libraries that we provide for different programming languages.
CellDesigner: A modeling tool for biochemical networks
SBML Editor since 2000
Development of the SBML ODE Solver Library (SOSlib) which basically integrates most of the functionality of libSBML and Sundials' solver library into a user friendly programing library. SOSlib provides a fine-grained user interface which makes it easy for a programmer to develop his/her applications.
Object-oriented modeling tool for dynamic and logical Systems-Biology models. Special interests are in model composition, handling of logical models and visual model representations.
SBML, libSBML, and all things SBML.
Building a new tool for SBML visualisation in Douglas Kells group at MIB. This is a new project, only just started, so no further details are available at this time...
CellDesigner: A modeling tool for biochemical networks + libSBML Java binding
SBML, libSBML, and all things SBML.
SOSLib : development of regularization methods for parameter identification MathSBML : implementation of inverse eigenvalue analyzer for probing possible dynamical behaviors
Advanced Interfaces Group, University of Manchester, EBI
The Virtual Cell is a physically consistent, mathematically rigorous, spatial modeling and simulation framework for cell biology. It provides a separation of layers representing biological models, physical mechanisms, geometry, mathematical models and numerical methods. This separation clarifies the impact of modeling decisions, assumptions, and approximations. The Virtual Cell has a rich, interactive user interface which connects to remote services providing scalable access to a modeling database and a large dedicated cluster for shared computation and storage. We continuously add new modeling capabilities, currently focusing on data/tool interoperability, model analysis, high performance/grid computing, and specialized standalone and plug-in tools.
BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests. Models present in BioModels Database are annotated and linked to relevant data resources, such as publications, databases of compounds and pathways, controlled vocabularies, etc.
In collaboration with Prof Kell's group and Prof Mendes, we are extending the UTOPIA visualisation and analysis framework to include an SBML viewer and editor. Our work comes from a background of computer science, human/computer interaction and high performance graphics, and we are aiming to use semantics and visualisation techniques to make SBML graphs legible and large graph comparison possible.
My work focuses on a number of distinct modeling processes related to model composition in SBML. The JigCell FusionWizard enables both fusing and/or composing two or more model flat models together. Model fusion is a process that combines two or more models in an irreversible manner. In fusion, the identities of the individual models (called submodels) being combined are lost, but the aggregated information remains the same. Model composition connects submodels together to generate a hierarchy of models. It turns out that there are significant similarities between model fusion and model composition, as we discovered during the process of building the fusion tool. The fusion process defines a series of steps taken to merge models together. This series of steps can be viewed as an 'audit trail' that can be used describe the set of instructions needed to connect/link the submodels for composition.
Is a member of the developing team of Smartcell. At the moment working on scripting languages for biochemical simulators, representation of 3D geometries and metabolism analysis.
The Virtual Cell: a physically based, spatially oriented modeling and simulation framework for cell physiology. SBML related work and goals: 1) working with the community to define new SBML Spatial Extensions. 2) acheiving MIRIAM compliance for VCell/VCML. 3) acheiving 100% VCell/SBML interoperability for common subset of functionality.
My work focuses on information management for the Manchester Centre for Integrative Systems Biology. This role covers both experimental data management and - perhaps more importantly - the 'glue' that allows the derived data to find its way into SBML models.