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Steve Gallo

Steve Gallo

Lead Software Engineer / Database Administrator

Steve has been with the Center for Computational Research since 2002. 

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 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.

Selected Supported Research Projects

  • 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. Thomas R. Furlani, et al, "Performance metrics and auditing framework for high performance computer systems" Proceedings of the 2011 TeraGrid Conference: Extreme Digital Discovery (TG11), 2011; doi:10.1145/2016741.2016759.
  2. Richard M Gronostajski, Joseph Guaneri, Dong H Lee and Steven M Gallo, "The NFI-Regulome Database: A tool for annotation and analysis of control regions of genes regulated by Nuclear Factor I transcription factors" Journal of Clinical Bioinformatics 2011, 1:4 doi:10.1186/2043-9113-1-4
  3. Steven M. Gallo, Dave T. Gerrard, David Miner, Michael Simich, Benjamin Des Soye, Casey M. Bergman, Marc S. Halfon, "REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila" Nucleic Acids Research 2010; doi:10.1093/nar/gkq999. PMID: 20965965
  4. Neeman, Alisa G., Gallo, Steven M., Efstathiadis, Efstratios, "Collaborative research in a regional grid" Gateway Computing Environments Workshop (GCE), 2010; doi:10.1109/GCE.2010.5676131
  5. Zihua Hu, Steven M. Gallo, "Identification of interacting transcription factors regulating tissue gene expression in human" BMC Genomics 2010, 11:49; doi:10.1186/1471-2164-11-49. PMID: 20085649
  6. Delmerico, J.A., Byrnes, N.A., Bruno, A.E., Jones, M.D., Gallo, S.M., Chaudhary, V., "Comparing the performance of clusters, Hadoop, and Active Disks on microarray correlation computations" Proceeds of the International Conference on High Performance Computing (HiPC) 2009 pp.378-387; doi: 10.1109/HIPC.2009.5433190
  7. 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. PMID: 18534077
  8. 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
  9. 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. PMID: 18039705
  10. 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. PMID: 18006570
  11. 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
  12. 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. PMID: 16303794
  13. 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
  14. Gallo, S.M., Miller, R., & Weeks, C.M., "The Design 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
  15. 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

Presentations:

2008 NYSGrid Fall Workshop