This site is a prelude to the internationally supported BioCatalogue system that will collect, store, validate, and make available web-services in the biosciences. This registry is mainly meant for the EU projects EMBRACE, BioSapiens and ENFIN, but other users are welcome too. As a potential web service user, you can search or browse the registry for services that match your needs. Furthermore, each entry includes live test data, showing the current and historical status of the service. Each entry can also include example client software to help you include them in your own programs or workflows. As a service provider, the registry helps you build high quality services that conform to industry standards, and gives you a means of advertising your tools to the user community as well as a platform for testing your service. Your service remains your property and published by you - this registry merely advertises its existence and its status.
This system will in due time merge seamlessly into the BioCatalogue, and if you use this registry, you will not have to register your service again with the BioCatalogue.
Recent News
MkDom2
MkDom2 is the program used routinely to build each new release of ProDom. The algorithm relies on the assumption that the shortest amino acid sequence corresponds to a single domain, and may be used as a query to screen the database with the psi-blast program, in order to cluster homologous domains. To build ProDom, we run this program on the UniProt (swissprot/trembl) Knowledge Database, but it can be run on any set of protein sequences in a fasta file.
Inputs:
- a file containing the sequences to analyse in fasta format
STREAM : A Practical Workbench for the Quantitative Modeling of Transcription
STREAM is the first publicly available framework for modeling, visualizing, and predicting the quantivative regulation of the transcription rate of a target gene.
Understanding transcriptional regulation of a gene in detail is a crucial step towards uncovering and ultimately utilizing the regulatory grammar of the genome. Modeling transcriptional regulation using thermodynamic equations has become an increasingly important approach towards this goal.
WSMPsrch
MPsrch is a biological sequence sequence comparison tool that implements the true Smith and Waterman algorithm. It allows an rigorous search in a reasonable computational time. MPsrch utilises an exhaustive algorithm, which is recognised as the most sensitive sequence comparison method available, whereas BLAST and FASTA utilise a heuristic one. As a consequence, MPsrch is capable of identifying hits in cases where BLAST and FASTA fail and also reports fewer false-positive hits.
ProDomCG_evoscen
ProdomCG_evoscen is a set of webservices allowing to browse ProDom-CG267 evolutionary scenarios. It includes
- GetScenarioProdom : takes an ProDom-CG family (CG + 6 characters) and returns its evolutionary scenario as a string of (number of nodes) characters (absence = 1, presence = 2)
- GetPresentFamiliesProdom : takes a taxID present in ProdomCG and returns a list of ProdomCG families present at this node
ProDomCG_tree
ProdomCG_tree is a set of webservices allowing to browse ProDom-CG267 phylogenetic tree. It includes
- NearestNodeProdom : takes an NCBI taxID and returns the closest taxID present in ProdomCG
- GetParentProdom : takes a taxID present in ProdomCG and returns its parent
- GetChildProdom : takes a taxID present in ProdomCG and returns its child(ren)
- GetDFStreeProdom : returns the list of all the taxIDs present in ProdomCG in DFS order