The Challenge

According to a report by The National Science Foundation (NSF), Blue Ribbon Advisory Panel on Cyberinfrastructure, "a new age has dawned in scientific and engineering research, pushed by continuing progress in computing, information, and communication technology, and pulled by the expanding complexity, scope, and scale of today's´ challenges.

The capability of this technology has crossed thresholds that now make possible a comprehensive ´cyberinfrastructure´ on which to build new types of scientific and engineering knowledge environments and organizations and to pursue research in new ways and with increased efficacy.

Such environments and organizations, enabled by cyberinfrastructure, are increasingly required to address national and global priorities, such as

• understanding global climate change,

• protecting our national environment,

• applying genomics-proteomics to human health,

• maintaining national security,

• mastering the world of nanotechnology, and

• predicting and protecting against natural and human disasters, as well as to

• address some of our most fundamental intellectual questions such as the formation of the universe and the fundamental character of matter."

The panel's recommendation is to establish an Advanced Cyberinfrastructure Program (ACP) to "create, deploy, and apply cyberinfrastructure in was that radically empower all scientific and engineering research and allied education."

Our Domain Expertise

ITC is already working on "Cyberinfrastructure" development projects. Our BioUML framework >> is based on the similar motivation - we are aiming to incorporate life science data on all levels starting from visual notation and all the way down to modeling of various processes.

Our team is involved in formalized description, visualization, simulation and analysis of complex biological systems. For example, mammalian cell-cycle regulatory networks in normal and pathological states. See: Systems Biology Modeling Team >>

Furthermore, we already have two frameworks that are ready for such projects:

1) BioUML >> is an open source extensible workbench based on Eclipse runtime from IBM. This framework is integrated with many biological databases and new databases can be easily added. BioUML supports many formats: SBML (level 1 and 2 completely,) CellML, GXL, BioPAX (under development). The BioUML project was partially funded by the Volkswagen Stiftung.

2) BeanExplorer Enterprise Edition >> is a perfect tool that provides a web based interface for biological database and analysis tools. BeanExplorer not only allows for the search and retrieval of biological information, it also has a web interface for database editing.  In one of Fedor Kolpakov ´s >>  publications on Bioinformatics >> he considers BeanExplorer Enterprise Edition better than SRS (Sequence Retrieval Systems) from LION Biosciences and explains why. As an example, you may want to take a look at the Cyclonet database >> This database is still under construction, however, you can get an idea of the web interface and its features. Contact us for a login and password to access Cyclonet >>

BioUML and BeanExplorer work together seamlessly: BioUML can be considered as "thick" client for biological databases and analyses methods and BeanExplorer provides the web based interface ("thin" client) for the same resources. Using this perfect pair we are currently developing the Biopath database  - a database for biological pathways and models, mainly related to cell cycle, cancer, oxidative stress.

The Solution - Collaborate with ITC

Our colleagues have the requisite programming skills and domain expertise to support any Cyberinfrastructure- and complex bioinformatics projects. We also offer database annotation / data entry specialists (i.e. biologists with IT training).  Our resources allow us to both

1. Develop sophisticated software solutions for clients requiring in-depth domain expertise, or

2. Provide additional resources to augment the client's resources:  Our client supplies the domain knowledge, prototype software, and ITC supports that subset of the client's software that the clients wants to put into production. ITC´s possible job list for the client could include, examples:

1. Development environment support

2.  "Harden" prototype code

   1. Usability

   2. Performance

      1. Speed

      2. Memory usage

   3. Maintainability

      1. Documentation

      2. Applying coding/development standards

3. Maintain existing software (bug fixes).  We would need to develop ground-rules in terms of who does what.

4. Help Desk

5. Production software support

Dedicated Science Center (DSC)

Our suggested model for such cooperations is our  Dedicated Science Center (DSC)

Similar to our RUSSIAN DEDICATED CENTER  (RDC), DSC is a facility of dedicated resources (Infrastructure & IT professionals) that act as a virtual extension to your present IT setup. Furthermore, you get a team that brings in extensive expertise in system biology methods to model complex biological systems.

Rates for scientific programmers under the DSC program are currently only $3,200/man-month. (Please note that rates depend on location and are subject to change without prior notice.)

We can easily scale up operations with the desired domain expertise within a few weeks/months. Please also bear in mind, that we are providing industrial strength enterprise application development for some of the largest corporations and institutions like the military in Russia. See references >>, e.g. Gazprom >>

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Russian Dedicated Center (RDC)
Dedicated Science Center (DSC)
Vertical Industry Expertise
Skills & IT Domains