Nencki Genomics Project

This is the documentation start page for the Nencki Genomics Project (NGP) - developing and maintaining a set (“an ecosystem”) of closely integrated tools for functional and regulatory genomics, consisting of:

  • Nencki Expression Webservice (NEWS) and its underlying Nencki Expression Database (NED)
  • Nencki Genomics Database (NGD) and its Nencki Genomic Webservice API layer
  • BNFinder Webservice (BWS) - a webservice providing Bayesian Analysis of Transcription Regulation, developed by the collaborating Computational and Systems Biology Group at the Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, who also develop BNFinder.
  • Galaxy Nencki Instance, providing a Galaxy-based web browser access to the above tools.

The above tools enable the user to analyze: gene expression data, genomic regulatory regions, and transcriptional co-regulation. Additionally, third-party webservice tools, integrated under Nencki Galaxy Instance, enable analysis of functional content of gene lists. The use of NGP tools is free and open to all users.

Nencki Expression Webservice and BNFinder Webservice (NEWS-BWS)

Nencki Expression Webservice (NEWS)

Nencki Expression Webservice (NEWS) provides functions for analysis of gene expression data: transformation, identification of differential expression, filtering, sorting, merging, subsetting, visualization, clustering and (optionally) intermediate results storage with access rights management. The data are passed between the NEWS functions in a unified XML object (NgpObject) format, permitting chaining of functional operations and unified programmatic access.

The documentation of NEWS and the tutorial on its use can be found here: Nencki Expression Webservice (NEWS)

NEWS template program (client) download

A python NEWS-BWS client (client_all_webservices.py) provides convenient access to the functions of NEWS and BWS. The client walks the user through the essential functionality of both services, while commented-out code provides templates for programmatic access to other functions. The NEWS-BWS client internally calls the BWS client (client_bnfinder.py), which must be present in the same directory. A second BWS client (client_bnfinder_get_result.py) serves to check the status and collect the results of NEWS-BWS submitted BWS jobs. The clients can be downloaded by clicking or copying and pasting into your browser the link below:

http://www.nencki-genomics.org/webservices/lib/exe/fetch.php?media=clients_news-bws_python.zip

In addition to python (we use python 2.7), these client requires installation of the python suds https://fedorahosted.org/suds.

BNFinder Webservice (BWS)

As the tool for the analysis of transcriptional co-regulation - permitting the user to take advantage of advanced Bayesian networks structural learning, we integrate Bayesian Analysis of Transcription Regulation Webservice - a specialized application build around the published BNFinder2 program. The documentation of BWS and the tutorial on its use can be found under this link: http://biquad.mimuw.edu.pl

Nencki Expression Database (NED)

The NEWS webservice users can use the Nencki Expression Database (NED) to store their intermediate or final tabular results. This use is optional and the full functionality of the NEWS webservice is available without login. NED can store rectangular numerical datasets of any shape, with any number of arbitrary row or column annotations. It is heavily normalized and intended for access primarily via dedicated NEWS webservice functions. It can also be accessed from a mysql client:

mysql -h www.nencki-genomics.org -u public.

The schema of the essential tables of NED can be found here. NED has the same advanced access control mechanisms as the published Nencki Genomics Database, maintaining user-submitted data private by default, permitting user management of the owned data and of the access rights to them.

Galaxy Nencki Instance

Third-party webservice tools

In addition to the webservices developed by us, this site provides integration and Galaxy interface to webservices for analysis of function and transcriptional co-regulation that were developed by other groups.
For the analysis of over-represented functional annotations, we integrate g:Profiler webservice function GOSt, developed by the BIIT group at the University of Tartu, Estonia. For selection genes with a particular Gene Ontology category we integrate QuickGO webservice, developed at European Bioinformatics Institute, and bioDBnet webservice function db2db, developed at Advanced Biomedical Computing Center, National Cancer Institute at Frederick, USA.
Transparently to the user, we leverage on Taverna server, developed at the School of Computer Science, University of Manchester, as middleware between the Galaxy and webservices, providing wide interoperability and rapid addition of new functionalities.

Nencki Genomic Database

The Nencki Genomic Webservice provides convenient access to the key functionality of the Nencki Genomics Database (NGD) plus visualization of the regulatory regions. The documentation of NGD webservices API and the tutorial on its use can be found here:
NGD webservice.

The extensive online documentation of NGD can be found here: Nencki Genomics Database wiki
You can also register there. Registration is only required only for adding and managing own data.



This site is maintained by the Laboratory of Bioinformatics of the Nencki Institute. Contact us

The project is supported by an infrastructural grant from the Polish Ministry of Regional Development POIG.02.03.00-00-003/09.

Documentation