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
  • Cloud/Grid Computing
  • Technical Project Management
  • Web Application Development
  • Data Warehouse Design
  • Machine Learning

 

Software Engineering:

Apply software engineering best practices to the development of scientific tools and facilitate sound development practices that lower the overall cost of long term software maintenance. CCR staff can serve as the technical project manager to provide continuity and enable best practices for projects as current students graduate and new students join research groups.

  • Software Requirements Gathering
  • Technical Project Management
  • Software Specifications
  • Iterative Design Methods incorporating user feedback

 

Programming:

Extensive expertise designing and implementing a wide variety of applications using a number of programming languages, design paradigms, and 3rd party 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 Application Development
  • Client-Server Architecture
  • Optimization

 

Database Design:

Support several research groups and manage datasets consisting of billions of rows and multiple terabytes of data.

  • Data Modeling, Schema Development, and Database Systems Management
  • MySQL, Oracle, Postgres, MongoDb

 

Selected Supported Research Projects

  • Aristotle Cloud Federation: A collaboration between Cornell University, University at Buffalo, and the University of California Santa Barbara to create a federated cloud in New York State and California and serve as a model for campus cyberinfrastructure that other institutions.
  • XDMoD: An open source tool to facilitate the management of high performance computing resources, widely deployed at academic, industrial and governmental HPC centers. Open XDMoD’s management capabilities include monitoring standard metrics such as utilization, providing quality of service metrics designed to proactively identify underperforming system hardware and software, and reporting job level performance data for every job running on the HPC system without the need to recompile applications. CCR hosts an XDMoD installation to provide accounting and job performance details for NSF's XSEDE portfolio.
  • Open OnDemand by OSC: An open source platform for HPC, cloud and remote computing access. We are enhancing resource utilization visibility by integrating the Open XDMoD platform to create a unified platform for scientists to both work and optimize their HPC work.
  • ColdFront: An open source resource allocation system designed to provide a central portal for administration, reporting, and measuring scientific impact of HPC resources. Coldfront was created to help HPC centers manage access to a diverse set of resources across large groups of users and provide a rich set of extensible meta data for comprehensive reporting.
  • IOTN Moonshot: The Immuno-Oncology Translational Network (IOTN) is a consortium to accelerate translation of basic discoveries to clinical applications to improve immunotherapy outcomes for both "hot" and "cold" cancers - and to prevent cancers before they occur.
  • REDfly: A curated collection of known Drosophila transcriptional cis-regulatory modules.
  • VIDIA: Data-intensive computing and analysis tool for SUNY students and faculty.
  • Caring Guidance: A program intended to provide information and support to guide women through the initial weeks to months after breast cancer diagnosis.
  • Breathe to Sleep: A program intended to provide information and support for people with sleep apnea who are using CPAP. This includes how to monitor your progress, manage your CPAP, troubleshoot problems, improve sleep and feel better.
  • 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.
  • Center for Relationship Marketing: Developing and applying new methods and tools to help enterprises create and capture values in the marketplace.

Publications:

  • Sperhac, Jeanette M. and Plessinger, Benjamin D. and Palmer, Jeffrey T. and Chakraborty, Rudra and Dean, Gregary and Innus, Martins and Rathsam, Ryan and Simakov, Nikolay and White, Joseph P. and Furlani, Thomas R. and Gallo, Steven M. and DeLeon, Robert L. and Jones, Matthew D. and Cornelius, Cynthia and Patra, Abani , "Federating XDMoD to Monitor Affiliated Computing Resources", Proceedings of the IEEE International Conference on Cluster Computing, IEEE Press. 2018, pp. 548--557 Belfast, UK.
  • Robin M. Lally and Kevin Kupzyk and Adam Mills and Steven Gallo and Karen Meneses, "Effects of social constraints and web-based psychoeducation on cancer-related psychological adjustment early-after breast cancer diagnosis", Journal of Psychosocial Oncology, Routledge. 2019, pp. 1-22. doi:10.1080/07347332.2018.1546787
  • Rivera, John and Keranen, Soile V E and Gallo, Steven M and Halfon, Marc S, "REDfly: the transcriptional regulatory element database for Drosophila", Nucleic Acids Research,2018, pp. D828–D834. doi:10.1093/nar/gky957
  • (https://dx.doi.org/10.1109/CLUSTER.2018.00074)", Proceedings of the IEEE International Conference on Cluster Computing, IEEE Press. 2018, pp. 548--557 Belfast, UK. doi:10.1109/CLUSTER.2018.00074
  • Nikolay A. Simakov and Martins D. Innus and Matthew D. Jones and Joseph P. White and Steven M. Gallo and Robert L. DeLeon and Thomas R. Furlani, "Effect of Meltdown and Spectre Patches on the Performance of HPC Applications", CoRR, Volume abs/1801.04329, 2018.
  • Wang, Fugang and Laszewski, Gregor von and Whitson, Timothy and Fox, Geoffrey C. and Furlani, Thomas R. and DeLeon, Robert L. and Gallo, Steven M., "Evaluating the Scientific Impact of XSEDE", Proceedings of the Practice and Experience on Advanced Research Computing, ACM. 2018, pp. 10:1--10:8 Pittsburgh, PA, USA. doi:10.1145/3219104.3219124
  • Simakov, Nikolay A. and DeLeon, Robert L. and Innus, Martins D. and Jones, Matthew D. and White, Joseph P. and Gallo, Steven M. and Patra, Abani K. and Furlani, Thomas R., "Slurm Simulator: Improving Slurm Scheduler Performance on Large HPC Systems by Utilization of Multiple Controllers and Node Sharing", Proceedings of the Practice and Experience on Advanced Research Computing, ACM. 2018, pp. 25:1--25:8 Pittsburgh, PA, USA. doi:10.1145/3219104.3219111
  • Jeanette M. Sperhac and Steven M. Gallo , "VIDIA: A HUBzero gateway for data analytics education", Future Generation Computer Systems, Volume 83, Elsevier. 2018.
  • Simakov, Nikolay A. and Innus, Martins D. and Jones, Matthew D. and DeLeon, Robert L. and White, Joseph P. and Gallo, Steven M. and Patra, Abani K. and Furlani, Thomas R., "A Slurm Simulator: Implementation and Parametric Analysis", High Performance Computing Systems. Performance Modeling, Benchmarking, and Simulation: 8th International Workshop, PMBS 2017, Denver, CO, USA, November 13, 2017, Proceedings, Springer International Publishing. 2018, pp. 197--217. doi:10.1007/978-3-319-72971-8_10
  • Nikolay A. Simakov and Joseph P. White and Robert L. DeLeon and Steven M. Gallo and Matthew D. Jones and Jeffrey T. Palmer and Benjamin D. Plessinger and Thomas R. Furlani, "A Workload Analysis of NSF's Innovative HPC Resources Using XDMoD", CoRR, Volume abs/1801.04306, 2018.
  • Sperhac, Jeanette and Deleon, Robert L. and Furlani, Thomas R. and Gallo, Steven M. and Innus, Martins and Jones, Matthew D. and Palmer, Jeffrey T. and Patra, Abani and Plessinger, Benjamin and Rathsam, Ryan and Nikolay Simakov, and Joseph P. White, and Thomas Yearke, "Managing Computational Gateway Resources with XDMoD", figshare. 2017. doi:10.6084/m9.figshare.5480458.v2
  • Fulton, Ben and Gallo, Steven and Henschel, Robert and Yearke, Tom and B\"orner, Katy and DeLeon, Robert L. and Furlani, Thomas and Stewart, Craig A. and Link, Matt, "XDMoD Value Analytics: A Tool for Measuring the Financial and Intellectual ROI of Your Campus Cyberinfrastructure Facilities", Proceedings of the Practice and Experience in Advanced Research Computing 2017 on Sustainability, Success and Impact, ACM. 2017, pp. 49:1--49:7 New Orleans, LA, USA. doi:10.1145/3093338.3093358
  • RM Lally, KA Kupzyk, SM Gallo, K Meneses, "SOCIAL CONSTRAINTS AND CARINGGUIDANCE PROGRAM EFFECTS ON PSYCHOLOGICAL ADJUSTMENT IN MONTHS AFTER BREAST CANCER DIAGNOSIS", Annals of behavioral medicine, Volume 51, 2017, pp. S2431--S2432.
  • Matthew D. Jones and Joseph P. White and Martins Innus and Robert L. DeLeon and Nikolay Simakov and Jeffrey T. Palmer and Steven M. Gallo and Thomas R. Furlani and Michael T. Showerman and Robert Brunner and Andry Kot and Gregory H. Bauer and Brett Bode and Jeremy Enos and William T. Kramer, "Workload Analysis of Blue Waters", CoRR, Volume abs/1703.00924, 2017,.
  • Simakov, Nikolay A. and DeLeon, Robert L. and White, Joseph P. and Furlani, Thomas R. and Innus, Martins and Gallo, Steven M. and Jones, Matthew D. and Patra, Abani and Plessinger, Benjamin D. and Sperhac, Jeanette and Yearke, Thomas and Rathsam, Ryan and Palmer, Jeffrey T., "A Quantitative Analysis of Node Sharing on HPC Clusters Using XDMoD Application Kernels", Proceedings of the XSEDE16 Conference on Diversity, Big Data, and Science at Scale, ACM. 2016, pp. 32:1--32:8 Miami, USA. doi:10.1145/2949550.2949553
  • Liu, B. and Childs-Disney, J. L. and Znosko, B. M. and Wang, D. and Fallahi, M. and Gallo, S. M. and Disney, M. D. , "{Analysis of secondary structural elements in human microRNA hairpin precursors}", BMC Bioinformatics, Volume 17, 2016, pp. 112. doi:10.1186/s12859-016-0960-6
  • DeLeon, Robert L. and Furlani, Thomas R. and Gallo, Steven M. and White, Joseph P. and Jones, Matthew D. and Patra, Abani and Innus, Martins and Yearke, Thomas and Palmer, Jeffrey T. and Sperhac, Jeanette M. and Rathsam, Ryan and Simakov, Nikolay and von Laszewski, Gregor and Wang, Fugang, "TAS View of XSEDE Users and Usage", Proceedings of the 2015 XSEDE Conference: Scientific Advancements Enabled by Enhanced Cyberinfrastructure, ACM. 2015, pp. 21:1--21:8 St. Louis, Missouri. doi:10.1145/2792745.2792766
  • G. von Laszewski and F. Wang and G. C. Fox and D. L. Hart and T. R. Furlani and R. L. DeLeon and S. M. Gallo, "Peer Comparison of XSEDE and NCAR Publication Data", 2015 IEEE International Conference on Cluster Computing, 2015, pp. 531-532. doi:10.1109/CLUSTER.2015.98
  • Gallo, Steven M. and White, Joseph P. and DeLeon, Robert L. and Furlani, Thomas R. and Ngo, Helen and Patra, Abani K. and Jones, Matthew D. and Palmer, Jeffrey T. and Simakov, Nikolay and Sperhac, Jeanette M. and Innus, Martins and Yearke, Thomas and Rathsam, Ryan, "Analysis of XDMoD/SUPReMM Data Using Machine Learning Techniques", 2015 IEEE International Conference on Cluster Computing, IEEE. 2015, pp. 642--649. doi:10.1109/CLUSTER.2015.114
  • Palmer, Jeffrey T. and Gallo, Steven M. and Furlani, Thomas R. and Jones, Matthew D. and DeLeon, Robert L. and White, Joseph P. and Simakov, Nikolay and Patra, Abani K. and Sperhac, Jeanette M. and Yearke, Thomas and Rathsam, Ryan and Innus, Martins and Cornelius, Cynthia D. and Browne, James C. and Barth, William L. and Evans, Richard T., "Open XDMoD: A tool for the comprehensive management of high-performance computing resources", Computing in Science and Engineering, Volume 17, Volume 4, IEEE Computer Society. 2015, pp. 52--62. doi:10.1109/MCSE.2015.68
  • Simakov, Nikolay A. and White, Joseph P. and DeLeon, Robert L. and Ghadersohi, Amin and Furlani, Thomas R. and Jones, Matthew D. and Gallo, Steven M. and Patra, Abani K., "Application kernels: HPC resources performance monitoring and variance analysis", Concurrency and Computation: Practice and Experience, Volume 27, Volume 17, 2015, pp. 5238--5260. doi:10.1002/cpe.3564
  • DeLeon, Robert L and Furlani, Thomas R and Gallo, Steven M and White, Joseph P and Jones, Matthew D and Patra, Abani and Innus, Martins and Yearke, Thomas and Palmer, Jeffrey T and Sperhac, Jeanette M and others, "TAS view of XSEDE users and usage", Proceedings of the 2015 XSEDE Conference: Scientific Advancements Enabled by Enhanced Cyberinfrastructure, 2015, pp. 21.
  • Velagapudi, S. P. and Gallo, S. M. and Disney, M. D. , "{Sequence-based design of bioactive small molecules that target precursor microRNAs}", Nat. Chem. Biol., Volume 10, Volume 4, 2014, pp. 291--297. doi:10.1038/nchembio.1452
  • Browne, James C. and DeLeon, Robert L. and Patra, Abani K. and Barth, William L. and Hammond, John and Jones, Matthew D. and Furlani, Thomas R. and Schneider, Barry I. and Gallo, Steven M. and Ghadersohi, Amin and Gentner, Ryan J. and Palmer, Jeffrey T. and Simakov, Nikolay and Innus, Martins and Bruno, Andrew E. and White, Joseph P. and Cornelius, Cynthia D. and Yearke, Thomas and Marcus, Kyle and Laszewski, Gregor and Wang, Fugang, "Comprehensive, open-source resource usage measurement and analysis for HPC systems", Concurrency and Computation: Practice and Experience, Volume 26, Volume 13, 2014, pp. 2191-2209. doi:10.1002/cpe.3245
  • Evans, Todd and Barth, William L. and Browne, James C. and DeLeon, Robert L. and Furlani, Thomas R. and Gallo, Steven M. and Jones, Matthew D. and Patra, Abani K., "Comprehensive Resource Use Monitoring for HPC Systems with TACC\_Stats", Proceedings of the First International Workshop on HPC User Support Tools, IEEE Press. 2014, pp. 13--21 New Orleans, Louisiana. doi:10.1109/HUST.2014.7
  • Wang, Fugang and von Laszewski, Gregor and Fox, Geoffrey C. and Furlani, Thomas R. and DeLeon, Robert L. and Gallo, Steven M., "Towards a Scientific Impact Measuring Framework for Large Computing Facilities - a Case Study on XSEDE", Proceedings of the 2014 Annual Conference on Extreme Science and Engineering Discovery Environment,ACM. 2014, pp. 25:1--25:8 Atlanta, GA, USA. doi:10.1145/2616498.2616507
  • White, Joseph P and DeLeon, Robert L and Furlani, Thomas R and Gallo, Steven M and Jones, Matthew D and Ghadersohi, Amin and Cornelius, Cynthia D and Patra, Abani K and Browne, James C and Barth, William L and others, "An analysis of node sharing on HPC clusters using XDMoD/TACC\_stats", Proceedings of the 2014 Annual Conference on Extreme Science and Engineering Discovery Environment, 2014, pp. 31. doi:10.1145/2616498.2616533
  • Lu, Charng-Da and Browne, James and DeLeon, Robert L. and Hammond, John and Barth, William and Furlani, Thomas R. and Gallo, Steven M. and Jones, Matthew D. and Patra, Abani K., "Comprehensive Job Level Resource Usage Measurement and Analysis for XSEDE HPC Systems", Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery, ACM. 2013, pp. 50:1--50:8 San Diego, California, USA. doi:10.1145/2484762.2484781
  • Furlani, T. R. and Schneider, B. I. and Jones, M. D. and Towns, J. and Hart, D. L. and Gallo, S. M. and DeLeon, R. L. and Lu, C. and Ghadersohi, A. and Gentner, R. J. and Patra, A. K. and Laszewski, G. and Wang, F. and Palmer, J. T. and Simakov, N., "Using XDMoD to facilitate XSEDE operations, planning and analysis", Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery (XSEDE '13), 2013, pp. 8. doi:10.1145/2484762.2484763
  • Browne, J. C and DeLeon, R. L. and Lu, C. and Jones, M. D. and Gallo, S. M. and Ghadersohi, A. and Patra, A. K. and Barth, W. L. and Hammond, J. and Furlani, T. R. and McLay, R. T., "Enabling Comprehensive Data-Driven System Management for Large Computational Facilities", Proceedings of SC13: International Conference for High Performance Computing, Networking, Storage and Analysis (SC '13), 2013, pp. 11. doi:10.1145/2503210.2503230
  • Furlani, T.R. and Jones, M.D. and Gallo, S.M. and Bruno, A.E. and Lu, C.D. and Ghadersohi, A. and Gentner, R.J. and Patra, A. and DeLeon, R.L. and Laszewski, G. and Wang, L. and Zimmerman, A., "Performance metrics and auditing framework using application kernels for high-performance computer systems", Concurrency and Computation: Practice and Experience, Volume 25, Volume 7, John Wiley \& Sons, Ltd. 2013, pp. 918. doi:10.1002/cpe.2871
  • Furlani, Thomas R. and Jones, Matthew D. and Gallo, Steven M. and Bruno, Andrew E. and Lu, Charng-Da and Ghadersohi, Amin and Gentner, Ryan J. and Patra, Abani and DeLeon, Robert L. and Laszewski, Gregor and Wang, Fugang and Zimmerman, Ann, "Performance metrics and auditing framework using application kernels for high-performance computer systems", Concurrency and Computation: Practice and Experience, Volume 25, Volume 7, 2012, pp. 918-931. doi:10.1002/cpe.2871
  • Gronostajski, R. M. and Guaneri, J. and Lee, D. H. and Gallo, S. M. , "{The NFI-Regulome Database: A tool for annotation and analysis of control regions of genes regulated by Nuclear Factor I transcription factors}", J Clin Bioinforma, Volume 1, Volume 1, 2011, pp. 4. doi:10.1186/2043-9113-1-4
  • Gallo, S. M. and Gerrard, D. T. and Miner, D. and Simich, M. and Des Soye, B. and Bergman, C. M. and Halfon, M. S. , "{REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila}", Nucleic Acids Res., Volume 39, Volume Database issue, 2010, pp. D118--123. doi:10.1093/nar/gkq999
  • Hu, Z. and Gallo, S. M. , "{Identification of interacting transcription factors regulating tissue gene expression in human}", BMC Genomics, Volume 11, 2010, pp. 49. doi:10.1186/1471-2164-11-49
  • Neeman, Alisa G.; Gallo, Steven M.; Efstathiadis, Efstratios, "Collaborative research in a regional grid", Gateway Computing Environments Workshop (GCE) 2010, 2010. doi:10.1109/GCE.2010.5676131
  • John Paul Walters, Vipin Chaudhary, Minsuk Cha, Salvatore Guercio Jr., Steve Gallo, "Comparison of Virtualization Technologies for HPC", Proceedings of the 21st IEEE International Conference on Advanced Information Networking and Applications (AINA-07) 2008, 2008. doi:10.1109/AINA.2008.45
  • Russ Miller, Jonathan J. Bednasz, Kenneth Chiu, Steven M. Gallo, Madhu Govindaraju, Michael Lewis, Catherine L. Ruby, Charles M. Weeks, "Grid-based research, development, and deployment in New York State", Proceedings of the 2008 IEEE International Symposium on Parallel and Distributed Processing, 2008. doi:10.1109/IPDPS.2008.4536205
  • Nagykaldi, Z. and Fox, C. and Gallo, S. and Stone, J. and Fontaine, P. and Peterson, K. and Arvanitis, T. , "{Improving collaboration between Primary Care Research Networks using Access Grid technology}", Inform Prim Care, Volume 16, Volume 1, 2008, pp. 51--58.
  • Halfon, M. S. and Gallo, S. M. and Bergman, C. M. , "{REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila}", Nucleic Acids Res., Volume 36, Volume Database issue, 2007, pp. D594--598. doi:10.1093/nar/gkm876
  • Griffith, O. L. and Montgomery, S. B. and Bernier, B. and Chu, B. and Kasaian, K. and Aerts, S. and Mahony, S. and Sleumer, M. C. and Bilenky, M. and Haeussler, M. and Griffith, M. and Gallo, S. M. and Giardine, B. and Hooghe, B. and Van Loo, P. and Blanco, E. and Ticoll, A. and Lithwick, S. and Portales-Casamar, E. and Donaldson, I. J. and Robertson, G. and Wadelius, C. and De Bleser, P. and Vlieghe, D. and Halfon, M. S. and Wasserman, W. and Hardison, R. and Bergman, C. M. and Jones, S. J. , "{ORegAnno: an open-access community-driven resource for regulatory annotation}", Nucleic Acids Res., Volume 36, Volume Database issue, 2007, pp. D107--113. doi:10.1093/nar/gkm967
  • 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, Volume 4743, Springer Berlin Heidelberg. 2007, pp. 273--284. doi:10.1007/978-3-540-74767-3_29
  • Gallo, S. M. and Li, L. and Hu, Z. and Halfon, M. S. , "{REDfly: a Regulatory Element Database for Drosophila}", Bioinformatics, Volume 22, Volume 3, 2006, pp. 381--383. doi:10.1093/bioinformatics/bti794
  • M. L. Green and S. M. Gallo and R. Miller, "Grid-enabled virtual organization based dynamic firewall", Fifth IEEE/ACM International Workshop on Grid Computing, 2004, pp. 208-216. doi:10.1109/GRID.2004.35
  • Gallo, Steven M. and Miller, Russ and Weeks, Charles M., "The Design of a Portable Scientific Tool: A Case Studying Using SnB", Proceedings of the 1996 ACM/IEEE Conference on Supercomputing, IEEE Computer Society. 1996, Pittsburgh, Pennsylvania, USA. doi:10.1145/369028.369035
  • Miller, Russ and Gallo, Steven and Khalak, Hanif and Weeks, C.M., "SnB: Crystal structure determination via Shake-and-Bake", Journal of Applied Crystallography, Volume 27, 1994, pp. 613-621.