Software tools, databases, formats and ontologies

These software tools, databases, formats and ontologies were produced by the lab or with significant contributions from members of the lab.

Software tools

 
JSBML

JSBML is a community-driven project to create a free, open-source, pure Java library for reading, writing, and manipulating SBML files and data streams.

Reference: Rodriguez et al. JSBML 1.0: providing a smorgasbord of options to encode systems biology models. Bioinformatics (2015) advanced online publication. [Europe PMC][Bioinformatics]

Contact: jsbml-development[at]googlegroups.com

MELTING

MELTING computes the enthalpy, the entropy and the melting temperature of the helix-coil transitions of nucleic acid duplexes.

Reference: Dumousseau et al. MELTING, a flexible platform to predict the melting temperatures of nucleic acids. BMC Bioinformatics (2012), 13:101. [Europe PMC][BMC Bioinformatics]

Contact: melting-forum[at]googlegroups.com

Meredys

Meredys allows for the simulation of multi-component, multi-feature state molecular species in two and three dimensions

Reference: Tolle et al. Meredys, a multi-compartment reaction-diffusion simulator using multistate realistic molecular complexes. BMC Systems Biology (2010), 4:24. [Europe PMC][BMC Systems Biology]

SBFC

The Systems Biology Format Converter aims to provide a generic framework to convert a Systems Biology model format into another.

Contact: sbfc-forum[at]googlegroups.com

SBpipe

SBpipe is a collection of software pipelines for systems modelling of biological networks. It currently provides pipelines for parameter estimation, time course model simulation and parameter scan.

Reference: Dalle Pezze and Le Novère. SBpipe: a collection of pipelines for automating repetitive simulation and analysis tasks. BMC Systems Biology (2017), 11:46. [Europe PMC][BMC Systems Biology]

Contact: sbpipe[at]googlegroups.com

SBMLeditor

SBMLeditor is a simple, low-level editor for SBML files. It allows you to manipulate SBML elements in a controlled way, whilst maintaining the validity of the final file.

Reference: Rodriguez et al. SBMLeditor: effective creation of models in the Systems Biology Markup Language (SBML). BMC Bioinformatics (2007), 8:79. [Europe PMC][BMC Bioinformatics]

Contact: biomodels-net-support[at]lists.sf.net

Databases

 
BioModels

BioModels is a repository of computational models of biological processes. Models described from literature are manually curated and enriched with cross-references. They are simulated to ensure reproducibility of results. All models are provided in the Public Domain.

Reference: Chelliah et al. BioModels: ten year anniversary. Nucleic Acids Research (2015) 43 (D1): D542-D548. [Europe PMC][Nucleic Acids Res]

Contact: biomodels-net-support[at]lists.sf.net

LGICdb

The Ligand-Gated Ion Channel database is a database recording the sequences of subunits of ion channel receptors. The database is now frozen and its last release was in 2007. We keep it alive for reference purposes.

Reference: Donizelli et al. LGICdb. A manually curated sequence database after the genomes. Nucleic Acids Researchh (2006) 34: D267-D269. [Europe PMC][Nucleic Acids Res]

MIRIAM Registry

The MIRIAM Registry provides a set of online services for the generation of unique and perennial identifiers, in the form of URIs. It provides the core data which is used by Identifiers.org.

Reference: Juty et al. Identifiers.org and MIRIAM Registry: community resources to provide persistent identification. Nucleic Acids Researchh (2011) 40 (D1): D580-D586. . [Europe PMC][Nucleic Acids Res]

Contact: biomodels-net-support[at]lists.sf.net

SynapseKB

SynapseKB is a set of maps describing signalling pathways of the glutamatergic synapse.

Standard formats

 
COMBINE

The 'COmputational Modeling in BIology' NEtwork (COMBINE) is an initiative to coordinate the development of the various community standards and formats for computational models. By doing so, it is expected that the federated projects will develop a set of interoperable and non-overlapping standards covering all aspects of modeling in biology.

Contact: combine-discuss[at]googlegroups.com

OMEX and the COMBINE archive

A COMBINE archive is a single file containing the various documents (and in the future, references to documents), necessary for the description of a model and all associated data and procedures.

Reference: Bergmann et al. COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project. BMC Bioinformatics [2014, 15:369]. [Europe PMC][BMC Bioinformatics]

Contact: combine-archive[at]googlegroups.com

SBGN

The Systems Biology Graphical Notation (SBGN) project, an effort to standardize the graphical notation used in maps of biological processes.

Reference: Le Novère et al. The Systems Biology Graphical Notation. Nature Biotechnology 27, 735 - 741 (2009). [Europe PMC][Nature Biotechnology]

Contact: SBGN Mailing Lists

SBML

The Systems Biology Markup Language (SBML), a free and open interchange format for computer models of biological processes.

Reference: Hucka et al. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics (2003) 19 (4): 524-531. [Europe PMC][Bioinformatics]

Contact: sbml-discuss[at]googlegroups.com

SED-ML

The Simulation Experiment Description Markup Language (SED-ML) is an XML-based format for encoding simulation setups, to ensure exchangeability and reproducibility of simulation experiments. It follows the requirements defined in the MIASE guidelines.

Reference: Waltemath et al. Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language. BMC Syst Biol 2011; 5: 198. [Europe PMC][BMC Syst Biol]

Contact: sed-ml-discuss[at]lists.sourceforge.net

Ontologies

 
BioModels qualifiers

The qualification of an annotation is important to grasp the relation between a model component and the resource used to annotate it. The relationship is rarely one-to-one, and the information content of an annotation is greatly increased if one knows what it represents rather than to knowing only that it is "related to". More details here.

Contact: combine-discuss[at]googlegroups.com

KiSAO

The Kinetic Simulation Algorithm Ontology (KiSAO) was developed describe existing computational simulation algorithms and their inter-relationships through their characteristics and parameters.

Reference: Courtot et al. Controlled vocabularies and semantics in systems biology. Molecular Systems Biology, 7:543 (2011). [Europe PMC][Molecular Systems Biology]

Contact: biomodels-net-discuss[at]lists.sf.net

MAMO

The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used in the life sciences (for the time being), the type of variables they use, the readout that can be expected and other relevant features.

Contact: mamo-ontology-discuss[at]lists.sf.net

SBO

The Systems Biology Ontology (SBO) is a set of controlled, relational vocabularies of terms commonly used in Systems Biology, and in particular in computational modelling. It consists of seven orthogonal vocabularies defining: reaction participants roles (e.g. "substrate"), quantitative parameters (e.g. "Michaelis constant"), classification of mathematical expressions describing the system (e.g. "mass action rate law"), modelling framework used (e.g. "logical framework"), the nature of the entity (e.g. "macromolecule"), the type of interaction (e.g. "process"), as well as a branch to define the different types of metadata that may be present within a model.

Reference: Courtot et al. Controlled vocabularies and semantics in systems biology. Molecular Systems Biology, 7:543 (2011). [Europe PMC][Molecular Systems Biology]

Contact: biomodels-net-discuss[at]lists.sf.net

TEDDY

The TErminology for the Description of DYnamics (TEDDY) project aims to provide an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology.

Reference: Courtot et al. Controlled vocabularies and semantics in systems biology. Molecular Systems Biology, 7:543 (2011). [Europe PMC][Molecular Systems Biology]

Contact: teddyontology-discuss[at]lists.sf.net