The CONNJUR Project Development Team

Note: Additional information about the scientists and software developers who have contributed to the CONNJUR Project will be posted shortly.

Current Projects

Spectrum Translation

Publications

1. Nowling RJ, Vyas J, Weatherby G, Ellis HJC, Gryk MR "The CONNJUR Spectrum Translator: Open Source software for converting the format of time-domain NMR data" XXIV^th International Conference on Magnetic Resonance in Biological Systems, Cairns, Australia, 2010
2. Nowling RJ, Vyas J, Weatherby G, Fenwick MW, Ellis HJC, Gryk MR "CONNJUR spectrum translator: an open source application for reformatting NMR spectral data" Journal of Biomolecular Nmr, May 2011
3. Ellis HJC, Nowlilng RJ, Vyas J, Martyn TO, Gryk MR "Iterative Development of an Application to Support Nuclear Magnetic Resonance Data Analysis of Proteins" 8^th International Conference of Information Technology: New Generations, Las Vegas, NV, 2011

Workflow Builder

Publications

1. Weatherby G, Vyas J, Nowling RJ, Ellis HJC, Gryk MR "CONNJUR Workflow Builder: Open Source software for spectral reconstruction of NMR data" 52^th Experimental Nuclear Magnetic Resonance Conference, Asilomar, CA, Apr. 2011.

History: Initial Initiatives

The CONNJUR Project was originally conceived as a software initiative by Dr.Michael Gryk from the University of Connecticut Health Science Center, Dr. Tim Martyn from Rensselaer Polytechnic Institute at Hartford and Dr. Heidi Ellis from Western New England College. After Drs. Gryk, Martyn and Ellis received a grant from the National Institutes of Health, several students from Rensselaer at Hartford worked on developing the initial data model and software application as part of their requirement for a Master's Degree in Computer Science. These students included Dr. Susan Fox-Erlich, Richard Giorgio, Gary Klesczewski, Robert Rapauch, George Rypysc and Jay Vyas.

The following presentations and publications resulted from these initial efforts

Development of a Data Model for Protein Structure

Presentations

1. Fox-Erlich SR, Gryk MR, Maciejewski M, Hoch JC, Balla S, Rajasekaran S, Schiller, MR. " Building Motif Lexicons" University of Connecticut, Department of Molecular, Microbial and Structural Biology Annual Retreat, Storrs, CT, March, 2006.
2. Fox-Erlich S, Ellis HJ, Martyn TO, Gryk MR. "StrucCheck: a Java Application to Derive Geometric Attributes from Arbitrary Subsets of Spatial Coordinates Obtained from the PDB". 46^th Experimental Nuclear Magnetic Resonance Conference, Providence, RI, Apr. 2005.
3. Raupach RE. "Using the CONNJUR Database to Analyze Atomic Bond Characteristics as they Relate to Surface Topology of Protein Molecules". 20^th Rensselaer at Hartford Computer Science Seminar Symposium, Hartford, CT, Apr. 2005.
4. Fox-Erlich S, Ellis HJ, Martyn TO, Skowronek S, Gryk MR. "Development of a Logical Data Model for NMR Molecular Structure Determinations". 1st New England Structure Symposium, Storrs, CT, Oct. 2004.

Publications

1. Fox-Erlich S, Martyn TO, Ellis HJ, Gryk MJ. Delineation and analysis of the conceptual data model implied by the "IUPAC Recommendations for Biochemical Nomenclature". Protein Sci. 2004 Sep; 13(9):2259-63.

Delineation of Architectural Requirements for Spectral Reconstruction Analysis in CONNJUR

Presentations

1. Giorgio, RJ. "Investigation of XML to Support an Application Framework for the Analysis of Structural NMR Data". 20^th Rensselaer at Hartford Computer Science Seminar Symposium, Hartford, CT, Apr. 2005.
2. Klesczewski GL. "Selecting a Software Architecture to Support a Framework for Data Processing Application Integration". 20^th Rensselaer at Hartford Computer Science Seminar Symposium, Hartford, CT, Apr. 2005.

Publications

1. Ellis HJC, Fox-Erlich S, Martyn TO, Gryk MR. "Development of an Integrated Framework for Protein Structure Determinations: A Logical Data Model for NMR Data Analysis". Third International Conference on Information Technology: New Generations (ITNG'06); pp. 613-18.
2. Verdi, K., Ellis, H.J.C., and Gryk, M.R., "Conceptual-level workflow modeling for NMR and other scientific experiments," BMC Bioinformatics, vol. 8, no. 31, Jan. 2007.

Initial Software Slice: Wrapping Spectral Reconstruction Software

Presentations

1. Gryk MR, Vyas J, Fox-Erlich S, Martyn TO, Ellis HJC. "CONNJUR: An Open Source Integration Environment for Biomolecular NMR Data Analysis". 47^th Experimental Nuclear Magnetic Resonance Conference, Asilomar, CA, Apr. 2006.
2. Gryk, MR. "CONNJUR: An Open Source Proposal for NMR Software Integration". Varian, Inc., Users' Meeting, Palo Alto, CA, Apr. 2006.
3. Ellis H.J.C., "Undergraduate Involvement in Bioinformatics Research: Lessons from the CONNJUR Project," The Eleventh Annual Conference on Innovation and Technology in Computer Science Education (ITiCSE), Bologna, Jun. 2006. (Poster)

Publications

1. Vyas J, Rypysc G, Ellis HJ, Martyn TO, Fox-Erlich S, Klesczewski GL, Giorgio RJ, Rapauch RE, Gryk MR. "CONNJUR: A Java Based Wrapper for NMR Pipe". Manuscript in preparation. 2006.
2. Gryk, M.R., Vyas, J., Schiller, M.R., Martyn, T. O., and Ellis, H.J.C., "CONNJUR: Practical Use of an NMR Integration Environment for Spectral Data Processing," 2009 Experimental Nuclear Magnetic Resonance Conference, Asilomar, CA, April 2009.

The following students and developers, in addition to Drs. Gryk, Martyn and Ellis, are continuing to develop the CONNJUR Project:

Development of a Pluggable Architecture for Integrating Spectral Reconstruction Software

Gerard Weatherby, contractor with Western New England University, is extending the component architecture framework , manages the CONNJUR build and test process, and contributed to the Spectrum Translator.

Jay Vyas, graduate student at University of Connecticut Health Center, designed and implemented the Workflow prototype and implemented the Varian subsystem of Spectrum Translator.

Matt Fenwick, graduate student at University of Connecticut Health Center, developed the Spectrum Translator Graphical User Interface.

Colbert Sesanker, contractor at University of Connecticut Health Center, is working on WorkflowBuilder. Colbert has implemented most of the WorkflowBuilder NMRPipe actors and is currently at work integrating Rowland Toolkit.

RJ Nowling worked with us as a research assistant during the summers of 2006, 2007, 2009, and 2010. He designed actor configuration GUIs for the Workflow prototype and designed the Spectrum Translator architecture and implemented the NMRPipe and Bruker subsystems. He is now pursuing a Ph.D. in Computer Science & Engineering at the University of Notre Dame with a focus in developing new computational methods for Molecular Dynamics.