Web Portal Development

From Chemical Informatics and Cyberinfrastructure Collaboratory

Contents

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Web Services and Workflows

This page collects standalone clients to various project Web Services. For a list of the services themselves, see Web Service Infrastructure for a collection of URLs to WSDL definitions. We also create entire scientific usage scenarios by using Workflow engines to combine several Web services. For Taverna examples, see Workflows.

We have additional, non-public services to BCI and OpenEye software that are available for Indiana University users.

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Portal

We are developing JSR 168 compliant portals and portlet components to provide user interfaces to Web Services and workflows. Our portal is available from http://www.chembiogrid.org/gridsphere and includes publicly available services (i.e. no login required).

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Standalone Web Apps

We have developed numerous standalone web interfaces to our services. These will be integrated into a comprehensive portal or start page in the future.

As a general rule, these are placed under http://www.chembiogrid.org/cheminfo/, so you can browse the listing there for services. Some specific examples include

  • Docking Database - an interface to the results of docking a drug-like subset of PubChem into a series of targets

http://www.chembiogrid.org/cheminfo/dock/

  • 3D structure Database - an interface to the 3D structures of nearly 10M PubChem compounds, obtained using MMFF94

http://www.chembiogrid.org/cheminfo/p3d/

  • PubChem Frequent Hitters - get a summary of how many assays a set of CID's are active and inactive in

http://www.chembiogrid.org/cheminfo/freqhit/fh

  • Scripps MLSCN Toxicity Predictions - obtain toxicity predictions based on a random forest ensemble using the Scripps MLSCN cytotoxicity data

http://www.chembiogrid.org/cheminfo/rws/scripps

  • ToxTree toxicity hazard predictions

http://cheminfo.informatics.indiana.edu/~rguha/code/java/cdkws/cdkws.html#tox

  • NTP DTP Anti-Cancer Activity Predictions - obtain predictions of whether a compounds will exhibit anti-cancer activity against the first 40 cell lines from the NCI DTP

http://www.chembiogrid.org/cheminfo/ncidtp/dtp

  • Ames Mutagenecity Predictions - predict whether a molecule will be mutagenic or not, based on a random forest model

http://www.chembiogrid.org/cheminfo/rws/ames

  • Pharmacokinetic Parameter Calculator - calculate pharmacokinetic parameters for drug like compounds

http://www.chembiogrid.org/cheminfo/pkcell/

  • Kemo - a natural language interface to PubChem

http://cheminfo.informatics.indiana.edu:8080/kemo/

  • Generate RSS feeds for PubChem queries

http://www.chembiogrid.org/cheminfo/rssint.html

  • Statistical Model Downloads - download predictive models in the R binary format

http://www.chembiogrid.org/cheminfo/rws/mlist

  • Miscellaneous cheminformatics web service clients - includes TPSA, 2D structure diagrams, and 2D similarity

http://cheminfo.informatics.indiana.edu/~rguha/code/java/cdkws/cdkws.html

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Even more Web Service Clients

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Varuna Web Service

These are sample clients. Clients for several more Varuna services are under development (see Web Service Infrastructure).

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VOTables Clients

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Stand Alone Programs

These programs are generally available as source code and in some cases have not been fully packaged. Some of these utilize or access PubChem and our derived databases via web services.

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