de.NBI-SysBio Services

COPASI

COPASI is an open-source software application for creating and solving mathematical models of biological processes such as metabolic networks, cell-signaling pathways, regulatory networks, infectious diseases, and many others. COPASI includes features to define models of biological processes, simulate and analyze these models, generate analysis reports, and import/export models in SBML format.
Funding: Development and maintenance partially funded by de.NBI.

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SABIO-RK

SABIO-RK is a manually curated database for biochemical reactions and their kinetic properties that is built for the needs of modellers. It describes participants and modifiers of the reactions, as well as measured kinetic data embedded in their experimental and environmental context. The structured and standardized data for metabolic and signalling reactions manually extracted from literature is annotated and linked to controlled vocabularies, databases and biological ontologies. SABIO-RK can be accessed via the database web interface offering full text and advanced search, and via web services for an automatic data search and integration into e.g. modelling and simulation tools. Data can be exported in standardized formats like SBML, SBPAX or simply in table or text formats. Find this service in BioTools here.
Funding: Development and maintenance partially funded by de.NBI.

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SABIO-RK service

Service for kinetic data extraction either from references or based on the specification of entities like reaction, enzyme, organism etc.. Extracted data can be viewed, accessed and exported in a structured way via SABIO-RK-web interface either in a public or private mode (for individuals or groups). Selected single or multiple data can be exported in SBML format, allowing a direct import into modelling tools. Vice versa, kinetic data stored in models in SBML-format can directly be uploaded to SABIO-RK database. Find this service in BioTools here.
Funding: Development and maintenance partially funded by de.NBI.

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SEEK

SEEK is a software platform for collaborative projects to support the data storage and data exchange between project partners. SEEK contains yellow pages including information about people, projects, institutes, and skills. Users are able to store, search, interlink and download information about experiments, models, Standard Operation Procedures (SOPs), investigations, studies, assays, biosamples, etc. Different levels of data security and privacy are implemented and allow controlled access of data and secure data sharing between project partners. SEEK has a web-based user interface as well as a RESTful web service interface for automatic access. SEEK is both available for local installation to share data within groups or they can use the FAIRDOMHub sharing space described below. For easy installation, virtual machine images of SEEK are available. SEEK is also available as openSEEK, a combination of the openBIS software from ETHZürich with the SEEK software. Find this service in BioTools here.
Funding: Development and maintenance partially funded by de.NBI.

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FAIRDOMHub, SEEK related services

The biggest running instance of the openSEEK software described above is the FAIRDOMHub - a Systems Biology Community Commons for independent researchers, projects and programmes, run by the transnational FAIRDOM project. This centrally hosted repository for managing and sharing systems biology research enables anybody to view, download and reuse published data and models. By creating an own project within the FAIRDOMHub the user can manage or publish own datasets, link them together, interlink them with mathematical models, protocols and publications and share them in a controlled manner within and across projects. NBI-SysBio provides support to projects that want to use the FAIRDOM Hub and/or SEEK for data management. This support includes help desk support ("how do I achieve?"), collecting requirements from the users, as well as training. If you are interested in such support, please use the contact link.
Funding: Development and maintenance partially funded by de.NBI.

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Excemplify

Excemplify is a web-based application that was developed to support the exchange and long-time storage of experimental data including work book spreadsheets and all associated data files. Information is automatically extracted in a configurable way and stored in a database. The data can be shared and exchanged between users but can be also stored and kept private for individual usage.
Funding: Development and maintenance partially funded by de.NBI.

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Rightfield

RightField is a software tool for adding ontology term selection to Excel spreadsheets. RightField is used by a 'Template Creator' to create semantically aware Excel spreadsheet templates. The Excel templates are then reused by scientists to collect and annotate their data; without any need to understand, or even be aware of RightField or the ontologies used. RightField is already tightly integrated with SEEK. Find this service in BioTools here.
Funding: Not de.NBI funded.

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BiVeS

BiVeS (Biochemical Version control System) is a software library (Plug in) for difference detection in versions of computational models in standard formats (SBML, CellML). It identifies the changes between two versions and provides both a formal (XML-encoded) and a visual (Graph ML) output of the differences.
Funding: Development and maintenance partially funded by de.NBI.

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MORRE

MORRE (Model Retrieval and Ranking Engine) is a Java-based library (Plug in) that offers novel search and ranked retrieval of models and associated simulation setups. It integrates information from different model repositories, bio-ontologies, and simulation setups. The ranking uses state-of-the-art Information Retrieval techniques. MORRE contributes to the process of finding computational models of interest.
Funding: Development and maintenance partially funded by de.NBI.

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CellNetAnalyzer (CNA)

CellNetAnalyzer (CNA) is a MATLAB toolbox providing various computational methods for analyzing structure and function of metabolic, signaling, and regulatory networks. For metabolic networks, CNA supports a variety of stoichiometric and constraint-based modeling techniques, including flux balance analysis (FBA), metabolic flux analysis, elementary-modes analysis, or computational strain design (e.g., minimal cut set analysis). Signal transduction and (gene) regulatory networks can be represented as logical networks (Boolean or multivalued logic) and as interaction graphs and be explored through logical steady state analysis (qualitative input-output behavior of signaling networks), minimal intervention sets, discrete simulations, simulation of logic-based ODEs (via ODEfy plugin) as well as analysis of global interdependencies and of feedback loops and signaling paths. Computations can be started within a GUI (interactive network maps) or from command line (via API functions).
Funding: Development and maintenance partially funded by de.NBI.

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COMBINE Archive Toolkit

The COMBINE Archive Toolkit consists of three software tools for developers and modellers who wish to create, explore, modify, and share COMBINE archives. (1) The CombineArchive library is an implementation of the COMBINE archive specification. It can be used by other software projects to support COMBINE archives. In addition, (2) a desktop application is available for offl ine usage; and (3) a web interface adds functionality for sharing archives online.
Funding: Not de.NBI funded.

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