Lead Software Engineer / Database Administrator

Center for Computational Research
NYS Center of Excellence in Bioinformatics and Life Sciences
University at Buffalo, SUNY
701 Ellicott St
Buffalo, NY 14203
Phone: 716-881-8960
Office: B1-107

Email Steve

Areas of Support

Software Engineering

CCR has the expertise to apply software engineering techniques to the development of scientific tools that facilitates sound development practices and the lowers the cost of long term software maintenance. CCR's staff can also provide software project management services and continuity to projects as students graduate and new students join research groups.

• Software Project Management and Lifecycle Management
• Software Requirements Gathering (including identification of stakeholders)
• Software Specification Writing
• Software Test Plans
• Iterative Design Methods incorporating user feedback

Programming

The software group has extensive expertise designing and implementing a wide variety of applications using a number of design paradigms and toolkits as well as knowledge of data structures that are necessary to efficiently process large amounts of information.

• Graphical User Interfaces (GUI)
• Service Oriented Architecture (SOA) and Web Services
• Web Portal Development
• Client-Server Architecture
• Multiple Programming Languages (C/C++, Perl, PHP, Java, JavaScript, FORTRAN)
• Markup-Languages (XML, SGML, HTML, etc.)
• Algorithm Optimization
• Database Integration

Database Design

CCR supports several research groups and manages datasets including billions of rows and terabytes of data.

• Data Modeling and Schema Development
• Database Systems Management
• Data Warehousing
• Oracle
• MySQL

Grid Computing

CCR staff is actively involved in many aspects of grid computing. For more information, see the CCR Grid computing page.

• Grid-Enabling software for research groups
• Maintaining grid infrastructure
• Cyberinfrastructure support
• Open Science Grid
• New York State Grid
• Condor

Selected Supported Projects and Research

• REDfly: A curated collection of known Drosophila transcriptional cis-regulatory modules.
• AAHSL Portal: A web-based portal for the collection, analysis, and presentation of electronic data collected via a survey of United States and Canadian academic health sciences libraries.
• Gamma Knife: The Gamma Knife procedure serves as an effective alternative to conventional neurosurgery or traditional radiation therapy in the treatment of certain brain disorders.
• New York State Grid (NYSGrid): An advanced collaborative technological infrastructure that supports and enhances the research and educational missions of institutions in New York State.
• Open Science Grid (OSG): OSG brings together computing and storage resources from campuses and research communities into a common, shared grid infrastructure over research networks via a common set of middleware.
• Grid Support Center: Supporting grid computing throughout New York State
• IMNEGEN: Collaboration with the National Institute of Genomic Medicine of Mexico to establish a framework for scientific collaboration between IMNEGEN and UB with a particular emphasis on bioinformatics, technological development and commercialization of products, as well as services that result from scientific research.
• Center for Relationship Marketing: Developing and applying new methods and tools to help enterprises create and capture values in the marketplace.
• WNYCHIP: Developing a community-wide consensus about the need for a WNY Healthcare Information Exchange system, as well as the structure it will take and its governance.
• Web portal development
• High availability application services
• Scalable support for large matrices in R
• Grid enabling of user applications
• University at Buffalo campus Condor flock

Publications

1. Zsolt Nagykaldi, Chester Fox, Steve Gallo, Joseph Stone, Patricia Fontaine, Kevin Peterson, "Improving collaboration between primary care research networks using Access Grid technology" Informatics in Primary Care 2008 16:51-58
2. John Paul Walters, Vipin Chaudhary, Minsuk Cha, Salvatore Guercio Jr., Steve Gallo, "Comparison of Virtualization Technologies for HPC" Proceeds of the 21st IEEE International Conference on Advanced Information Networking and Applications (AINA-07) 2008
3. Marc S. Halfon, Steven M. Gallo, Casey M. Bergman, "REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila" Nucleic Acids Research 2008 36:594-598; doi:10.1093/nar/gkm876
4. Obi L. Griffith, et al, "ORegAnno: an open-access community-driven resource for regulator annotation" Nucleic Acids Research 2008 36:107-113; doi:10.1093/nar/gkm967
5. Jonathan J. Bednasz, Steven M. Gallo, Russ Miller, Catherine L. Ruby, Charles M. Weeks, "Grid Computing in New York State, USA", Frontiers of High Performance Computing and Networking ISPA 2007 Workshops 2007 4743:273-284; doi:10.1007/978-3-540-74767-3_29
6. Steven M. Gallo, Long Li, Zihua Hu, and Marc S. Halfon, "REDfly: a regulatory element database for Drosophila" Bioinformatics 2006 22:381-383; doi:10.1093/bioinformatics/bti794
7. Green, M.L, Gallo, S.M, Miller, R, "Grid-Enabled Virtual Organization Based Dynamic Firewall", GRID '04: Proceedings of the Fifth IEEE/ACM International Workshop on Grid Computing (2004):208-216; doi:10.1109/GRID.2004.35
8. Gallo, S.M., Miller, R., & Weeks, C.M., "The Development of a Portable Scientific Tool: A Case Study Using SnB" Proceedings of the 1996 ACM/IEEE conference on Supercomputing 1996; doi:10.1145.369028.369035
9. Miller, R., Gallo, S.M., Khalak, H., & Weeks, C.M., "SnB: Crystal Structure Determination via Shake-and-Bake" Journal of Applied Crystolography 1994 27:613-621; doi:10.1107/S0021889894000191

Biographies

Presentations