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Frequently Asked Questions
What is Biomodels Database?BioModels Database is a repository of curated quantitative biological models that have been described in peer-reviewed scientific publications. Models are annotated and cross-referenced with relevant external data resources, such as publications, databases of compounds and pathways, ontologies, etc. The curation process ensures that the provided models are syntactically correct and valid with respect to their encoding format. In addition, there is a verification of the logical model composition, the accuracy of the biological information contained in the model, as well as confirmation that the model published will, within reasonable bounds, reproduce the behaviour attributed to it. Users can browse and search the content of the repository, and download models in SBML format, as well as various other formats, such as XPP, VCML, SciLab, Octave, BioPAX, PNG, SVG, ... A human readable summary of each model is also available in PDF. BioModels Database is a project of the BioModels.net initiative. More information can be found in the associated publications. How does BioModels Database differ from other databases of models?BioModels Database is more than just a repository of models, it is a true database. The models, their controlled annotation and all related information is stored in a set of MySQL tables. This allows users to search not only for particular models based on their internal components elements, but also based on the extensive additional annotation. In addition, this annotation allows the exploration of the relevant linked resources, thereby facilitating the understanding of the concepts upon which the model is founded. Hoes does BioModels Database differ from other biological pathway databases?BioModels Database is not a database of biochemical pathways. The current state of the field of Computational Systems Biology means that these models are largely dominating the resource at the moment, but the scope of BioModels Database itself is larger than just biochemical events. A quantitative model also differs from a pathway in several respects:
How does BioModels Database differ from Reactome?Reactome is a database of reactions and pathways, not a database of quantitative models. The SBML files exported by Reactome (or KEGG for that matter) do not contain any quantitative information, whether quantities (amount or concentration of species) or kinetics. Reactome aims to describe the human cellular pathways accurately and in great details, not to distribute abstract quantitative description of their functions. How to cite BioModels Database?Please, have a look at the citation information page. How to cite a model present in BioModels Database?The best way to cite a model present in BioModels Database is to state the reference publication associated with the model. You can also mention the model's identifier (of the form "BIOMD" or "MODEL" followed by 10 digits). How to contact the team behind BioModels Database?The easiest way to contact the team developing and maintaining the software infrastructure and the content of BioModels Database is to use the following email address: biomodels-net-support AT lists.sf.net. You can also refer to the information provided on the contact us page. I wish to contact the original author(s) of a model, but the listed email does not work. What should I do?This will happen occasionally as people move on to new roles or to new positions in different institutions. There is no easy solution for this, so we would suggest in the first instance to write to the BioModels Database curation team, which can have them look into it on your behalf. Please provide as much information as you have available, and avenues you may have explored already. The curation team can be contacted via: biomodels-cura AT ebi.ac.uk. How reliable are the models hosted in BioModels Database?Before being publicly available on BioModels Database, a model passes through a curation pipeline. This ensures its syntactic correctness, semantic soundness, and its correspondence with its reference publication, both in terms of model structure and simulation results. Consequently the structure of a model would not normally change, while its annotation is expected to improve constantly over time. What should I do if I find an error in a model?The models present in BioModels Database have already been extensively checked and corrected. However, it remains possible that some errors may have crept through our rigorous curation pipeline. If you discover any errors with a specific model, or have any potential concerns, please do contact us. Comments and bugs for specific models may be submitted directly from the menu bar at the top of the web page describing each model, where you will find a "Submit Model Comment/Bug" link. What are the conditions of use and distribution for unmodified models originating from BioModels Database?You can use and freely distribute the models present in BioModels Database in their current form. Please refer to the legal terms of use for more details. What are the conditions of use and distribution for modified models that originated from BioModels Database?You can modify and freely distribute a modified version a model, in whole or part, that is present in BioModels Database. The modified model must be renamed, and all references to the BioModels Database identifier and any mention of the copyright holders of the model must be removed. This is to prevent any confusion over precisely which is the original model, and which are modified versions of that model. Please refer to the legal terms of use for more details. Can I convert a model from BioModels Database into another SBML version?Yes, you can convert a model coming from BioModels Database from the original SBML Level/Version to another, and distribute the converted version freely. In these instances, the converted model is regarded as a modified version. Hence, the converted model must be renamed, and all references to the BioModels Database identifier and any mention of the Copyright Holders of the model must be removed. This is to prevent any confusion over precisely which is the original model, and which are modified versions of that model.Please refer to the legal terms of use for details. For models from the curated branch, you can download them in multiple Levels and Versions of SBML via the "Download SBML" link present on top of each model page. How to browse and search BioModels Database?There are two main ways in which the BioModels Database can be browsed:
Once you have identified a model of interest, you can click on the link (on its identifier) to reach the model description page. Access to further information is offered here through a variety of tabs. What information can be found using the model tabs?Here is a brief description of the information available through each of the tabs available on each curated model description page:
How to download a model from BioModels Database?There are several way to download the models:
What options are available for simulating a model?Several options are available to simulate the models: All models in the curated branch can be simulated via the embedded online simulation feature. This can be launched via the "BioModels Online Simulation" item in the "Actions" top menu. Simulations are performed using the SBML ODE Solver Library (SOSlib) and run on the EBI computing cluster. Both the numerical results and a graph are provided to the user once the simulation is complete. 
Many models stored in the curated branch have been converted to the JWS Online format and can be simulated with its mathematica-based Java applet. This option can be launched via the "BioModels Online Simulation" item in the "Actions" top menu. Also refer to the full list of models from BioModels Database which can be simulated in that way. 
Models are exported into several different formats, that can be used with various simulators. Some of the formats are specific for particular software tools, such as XPP-Aut or SciLab. Other formats, such as SBML and CellML are common standard formats and can be used with multiple compliant software tools. Once a model has been selected, it can be downloaded using the relevant link from the "Download SBML" or "Other formats" menus, and saved locally. The model can then be simulated using your simulation tool of choice. Below are screenshots of Tyson1991_CellCycle_6var model simulated using JWS Online, SciLab, XPP-aut, COPASI and CellDesigner. 
How to generate a sub-model from a larger one?BioModels Database provides a feature which allows users to extract components from large scale models into smaller sub-models. From the "Overview" tab, one can select reactions, entities and parameters (via the check-box alongside them) and generate a sub-model containing these specific elements. Once all the elements of interest have been selected, please click one the "Create a submodel with selected elements" link at the top of the tabbed display. After generation, the newly generated sub-model will be available from a newly created tab and can be downloaded in SBML format. 
Be aware that the generated sub-models might contain more elements than the ones selected. This is due to the fact that the generation algorithm ensures that the sub-model is coherent and valid SBML. Does BioModels Database provide SBGN maps?BioModels Database provides graphical representations of the models in various formats (PNG, SVG and a dynamic visualisation via a Java applet). Those are available from the "Actions" menu. 
Due to workforce limitations, and the volume of work that generating SBGN exports necessitate, the layout of most of these maps is not currently fully compliant with the specification of SBGN Process Diagrams Level 1 Version 1. However, the BioModels.net team has been involved in SBGN development since it's inception, and is fully committed to support it as much, and as quickly, as possible. Why doesn't BioModels Database export models under MATLAB format?BioModels Database developers are doing their best to provide a variety of export formats. BioModels Database is a public resource, part of the BioModels.net initiative, and is totally committed to support open standard formats. Therefore, our first priority is the support of free (non-proprietary) software. In addition, BioModels Database is entirely funded by taxpayers' money, and we feel it is inappropriate to develop software to interface with commercial tools as a priority. That said, if you are a user of MATLAB and want to use BioModels Database models with this software, there exist several packages offering SBML support for MATLAB. See the SBML Toolbox, the Systems Biology Toolbox, and simbiology, the toolbox developed by MathWorks. How to submit a model?Anybody can submit a model to BioModels Database. Even if you are not the actual author or encoder of a model you can submit it for inclusion in BioModels Database. If you do so, you will be recorded as the submitter, not as an author or an encoder. However, we do encourage you to contact the original authors to be sure they are happy with the submission. If a model is encoded in SBML or CellML, the submission is entirely processed online, via the submission page. If the model is encoded using a different format, please read the section of this FAQ about the supported formats. If the model can be converted into SBML or CellML, please contact us. Once the model has been submitted, the submitter will receive an email notification with a unique, stable and perennial submission identifier. This identifier is composed of the string "MODEL" followed by 10 digits, for example MODEL1003250000 (these digits are actually based on the submission date and time). This identifier can be used to reference the model in publications, and once the model is publicly available on BioModels Database, users can directly access the model using this identifier. BioModels Database currently only publishes models which have been described in a peer reviewed scientific publication. Therefore, authors are encouraged to submit models before publication of the associated paper (and will receive an identifier that they can used in the publication), but the models will only be publicly available on BioModels Database once the paper has been published. In order to access a model, knowing it submission identifier, you can use the URL: http://www.ebi.ac.uk/biomodels-main/ followed by the identifier. For example: http://www.ebi.ac.uk/biomodels-main/MODEL1002160000. Can I submit a model before it is described in a published paper?Yes. Models can be submitted prior to the publication of the associated paper(s). It is actually strongly advised to do so: at the submission time, each model is assigned a unique and perennial identifier which allows users to access and retrieve it. This identifier can be used by authors as a reference in their publications. Please refer to the section of this FAQ about the access to a model after its submission for more information about when a model will be publicly available from BioModels Database. Will a model be publicly accessible immediately after its submission?No. Models are not directly visible and retrievable by the public as soon as they are submitted to BioModels Database. From submission to their public release, all models undergo various automated and manually performed curation and annotation steps to ensure a consistent level of quality and accuracy. Moreover, all models are only made publicly available from BioModels Database after the publication of the corresponding papers. If you submitted a model before the publication of the associated paper, please keep us informed of the status of your publication. That way, we can make the model available from BioModels Database as quickly as possible. Finally, new models are usually made publicly available during "releases". There are between 2 to 4 releases of the database a year. Please contact us if you need your model to be available earlier. Can reviewers access unpublished models?BioModels Database can provide access to unpublished models to reviewers. This is not automatic, so the model submitter needs to request it (for example emailing us at biomodels-cura AT ebi.ac.uk or mentioning it in the comment field of the submission form). In this case, we will provide the submitter with a URL which can be used to download the model encoded in SBML. If security is a concern, we can supply a protected access, where reviewers will be asked for a password to access the model. If you have more specific needs, please don't hesitate to contact us. Could BioModels Database accept models encoded using my own software-specific format?Currently BioModels Database can only cover a subset of the modelling formats landscape. While there have been requests to increase the number of model formats that are accepted in BioModels Database, the underlying strategy of BioModels Database is to accept and distribute models in semantically rich but standard formats. This is to improve model accessibility, sharing and distribution for the larger community. Since BioModels Database curators simulate models in various software, in order to verify the reproducibility of the results, a format common to the simulation software is required. For these reasons, only models models encoded using SBML and CellML are currently accepted. However, numerous conversion tools exist (such as SBFC), which allow one to transform models into supported standard formats. How to submit a revised version of a model?
Why does my SBML model contain no species or reactions after a conversion from CellML?The issue is that there is no annotation in the CellML file that could help the converter to determine if a certain variable is a SBML species, parameter or compartment. And the same applies to any CellML equation. The current version of the converter is not trying to do any complicated guesses and therefore converts every CellML variable into a SBML parameter and all the equations into rules. We are currently trying to define some annotations that would allow to create better SBML files from CellML and vice-versa, the ultimate goal would be to be able to do a round-trip conversion, starting either from a SBML model or a CellML model, without loosing any information. Why do I receive error messages when trying to submit a model?Sometimes, trying to submit a model to BioModels Database with the submission interface results in an error message of the type:
Unable to successfully complete the submission of the model contained within the file:
C:\Documents and Settings\user\models\My Model.xml
due to the following errors:
org.w3c.dom.ls.LSException: no protocol:
/ebi/research/compneur/WWW/biomodels/models-main/uplo/C:\Documents and Settings\user\models\My Model.xml
This problem is due to a bug in certain versions of Microsoft Internet Explorer which do not correctly strip the file path before the filename. Commonly, this type of error may be seen in browsers where all image links are broken, and point to the original location, for example of the webdesigner's local disk. In these instances, we would advocate the use of a different web browser. There are several free open source alternative one that are available for all platforms, such as Firefox or Seamonkey. What is annotation, and what purpose does it serve in a model?Model elements can describe a plethora of different entities, such as genes, proteins or metabolites. The usage of free text or non-standard nomenclature to identify those elements is not reliable, as it can introduce ambiguity to the model components, such that subsequent users of a model would struggle to identify the precise entities involved. Annotation is useful to identify model elements. This ensures that users will be able to understand the models and increases the possibility of their reuse. Moreover, annotation is a key element for processes such as data comparison, data integration and data conversion. Finally, this also allows provision of accurate search engines (BioModels Database makes heavy use of annotation when users search for models of interest). Models in BioModels Database are provided with consistent annotation using unambiguous identifiers. Those identifiers are generated by the MIRIAM Registry and Identifiers.org services. They can be used to reference records from external databases (such as Taxonomy, EMBL-Bank or UniProt), terms from ontologies (such as Gene Ontology, SBO or ChEBI), publications, etc. What checks are performed to ensure model correctness?Before being made publicly available through BioModels Database, models are thoroughly verified. This involves several types of checks, some automated and some manually performed by a team of curators. The following checks are performed:
Who annotates the models?The models are annotated by the BioModels Database curation team. However, proposed annotation can be submitted directly with a model using the annotation scheme developed for SBML (since Level 2 Version 2). This annotation scheme is supported by numerous tools. What is MIRIAM?MIRIAM is the Minimum Information Required in the Annotation of Models (Press Release). Initiated by the BioModels.net project, it is a set of guidelines defining how a model should be encoded and annotated in order to be successfully distributed, exchanged and ultimately reused. In particular MIRIAM requires that a model provides all the information necessary to instantiated in a simulation, such as the initial conditions. In addition, the reaction graph generated from this simulation must reproduce the results of the original publication, in which the model was first described. Moreover, the MIRIAM guidelines require that all model components contain sufficient controlled annotation such that each component can be unambiguously identified. The MIRIAM Registry and Identifiers.org have been developed specifically to provide generation and resolution services for unique and perennial identifiers to be used in controlled annotations. All models stored in the curated branch of BioModels Database are MIRIAM-compliant. How is MIRIAM compliance ensured?All the models in the curated branch are fully MIRIAM compliant, and hence well annotated. MIRIAM compliance is confirmed for models in the curated branch of the Database since each of the requirements is satisfied in the following way:
How are annotations stored in SBML?The annotation of each model component is stored in the corresponding SBML element using the a scheme initially designed by Nicolas Le Novère and Andrew Finney, and now part of SBML (since Level 2 Version 2). It relies on the use of RDF, Dublin Core, vCard and the BioModels.net qualifiers. 
Please refer to the SBML specification for more information about the annotation scheme. When is a model completely annotated?Annotating each model component with the most relevant resource records takes great efforts, especially since the number of submitted models has grown rapidly. For example, the 21st release of BioModels Database (8th February 2012) contains 106,210 cross-references (links to external resources contained in the annotations). This number need to be compared with the total number of species (130,800) and relationships (151,274 this number including reactions, rate rules, events and assignment rules) involved in the existing 829 models. Therefore annotations can can always be improved. Besides manpower limitations, this discrepancy is sometimes due to a lack of adequate or suitable resources for annotation, for instance for molecular entities which are created only for simulation purposes. Moreover, biological data resources are often slightly lagging behind newly generated knowledge, and it is possible that a particular resource does not offer the relevant information at the time the model is annotated. In the case of hierarchical controlled vocabularies, such as Gene Ontology or ChEBI, there is the option to use a term at a higher level of abstraction if the required precise term does not currently exist. Most often, one can always add some information, even if not optimal. Hence, model annotation needs to be, and indeed is, a continuous process. What are the tools used by the curators of BioModels Database?Our curators use a wide range of tools to perform their curation tasks: CellDesigner, COPASI, Jarnac, MathSBML, RoadRunner, SBMLOdeSolver, SBMLeditor, SemanticSBML, JigCell, XPP-Aut, ... Moreover, they also use tools such as Gnuplot and various custom scripts. What is the non-curated branch of BioModels Database?The success and rapid growth of BioModels databases has led to a couple of issues, both of which are handled using the non-curated branch of BioModels Database. Firstly, BioModels Database faces an ever-growing, and increasingly complex, number of model submissions which are growing at a pace that exceeds our curation capacity. Secondly, many of the models submitted, while syntactically correct, cannot be curated for various reasons. Hence, the non-curated branch of BioModels Database is a public holding area for models that have yet to be curated, or cannot be curated for various reasons. The models held in the non-curated branch are of four types:
Note that all the models in the non-curated branch have nevertheless passed the XML check, SBML syntax check and SBML consistency checks. What are the tools used to develop and run the software infrastructure behind BioModels Database?The infrastructure is powered by Apache Tomcat, the web services use Axis, the database runs MySQL, the search is powered by Lucene, ... For more information about the software infrastructure, please refer to:
BioModels Database makes use of many third-party free software such as: libSBML, JSBML, Lucene, Xalan, Xerces, Paxtools, ... A new open community project has been launched: Jummp. It aims to provide the next generation model management platform and will ultimately be used as the software platform behind BioModels Database, as well as other projects and communities. Can I install my own version of BioModels Database?The models can be freely reused and the software running BioModels Database itself is an open source project distributed under the GNU General Public License. For more information, please refer to the software infrastructure entry of this FAQ. All converters are also available under an open source license and can be downloaded from the download section of the BioModels SourceForge repository. In order to store your own models or just plug part(s) of the BioModels Database infrastructure into your own, you'll need to setup your own local instance of the repository. In order to help you through this procedure, we created the following page: development with BioModels Database source code. What is the naming and identifier scheme used in BioModels Database?During the curation process, the curators will give an appropriate name to each model. This follows the general scheme: AuthorYear_Topic_Method. For example, Edelstein1996_EPSP_AChEvent refers to the model BIOMD0000000001. At the time of submission, a unique submission identifier assigned to the model. It is composed of the character sequence "MODEL" followed by ten digits extracted from the timestamp of submission. When a model is moved to the curated branch, a new model identifier is generated and assigned to it. This identifier is composed of the character sequence "BIOMD" followed by ten digits reflecting the model's position in the branch (for example "BIOMD0000000216" for the 216th model successfully curated). Both identifiers are unique and permanent, and will never be re-assigned to a different model, even if for some reason a particular model must be retracted from the database. Both identifiers can be used to retrieve the model and quoted in subsequent publications. Who are the authors of a model?The authors of a model are the individuals who initially described the model in a peer-reviewed publication. Who is the submitter of a model?The submitter of a model is the person who actually submitted the model and therefore requested its addition in BioModels Database. Anybody can submit a model to BioModels Database. Please refer to the submission procedure, if you want to know more. Who are the encoders of a model?The encoders of a model are the individuals who actually encoded the model in its present form, based on the published article. These individuals could be the authors of the publication, members of the curation team, or any other scientists who decided to encode the published article. Why do I get an error message stating some reaction modifiers are not declared?Some models contain reactions where the kinetics are modified by compounds that are not themselves reactants. These compounds are not consumed or produced by the reaction, and are known as modifiers. This error occurs when some software tools do not explicitly list the modifiers contained in the model reactions. A consistency check has been implemented to identify missing modifier declarations, and is now applied to all models submitted to BioModels Database. This error should not happen anymore. Why do I see a "session has expired" message when browsing the resource?If you see a message stating "Your session has expired. Please reload the main model page." while browsing the database or trying to submit a comment or a bug report about a specific model, please first check that you are using the proper URL to access the resource (the string "compneur-srv" should not be present in the URL).
For example, if you were using:
If that does not solve your problem, please contact us, mentioning the URL you were using. 
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Computational Systems Neurobiology Group, European Bioinformatics Institute.
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