Reaching Others University at Buffalo - The State University of New York
Skip to Content

Consulting

As a part of its mission to enable research and scholarship at UB, CCR provides users with a wide range of consulting services in areas that include parallel computing, software engineering, scientific and medical visualization, bioinformatics, cloud computing, advanced database design and data mining, urban simulation and modeling, computer animation, and cluster management. In addition, the software engineering group have extensive experience in custom software development, including GUI and web-based interfaces. For additional information on these services or how CCR can help facilitate your research, please contact us.

 

Scientific Computing/Modeling

Consulting on all aspects of parallel computing, including software development, parallel computing architecture design, cluster management, parallel file systems, and high-speed networks. Specific areas of expertise include parallel algorithm development, advanced software profiling and debugging tools, message passing (MPI) and shared memory (OpenMP) based parallel computing, performance tuning, scientific programming, and Linux based cluster management. A course on high-performance computing is also offered. Past projects have included:

  1. Assisted development of scalable parallel algorithms in medical imaging
  2. Evaluation of viability and performance tuning of commercial and open-source quantum chemistry applications
  3. Performance evaluation of competing hardware and software technologies for high-performance computing applications
  4. Performance improvements through the development of detailed performance models
  5. Development of dynamic, data-driven applications

 

Molecular Modeling

Consulting on all aspects of molecular modeling (computational chemistry) for chemistry, biology, and materials science based applications, including protein chemistry, gas phase molecular clusters, zeolites, etc. Properties calculated include molecular geometry, reaction profiles, vibrational and electronic spectra, relative energetics, conformational analysis, electron density, electrostatic potential, and molecular orbitals, etc. Methods employed include quantum mechanical based methods (Q-Chem, GAMESS, and NWCHEM, etc), molecular mechanics methods (AMBER, CHARMM, etc), and molecular dynamics simulations. A graduate level sequence on Computer Modeling of Biological Systems is also offered.

 

Software Engineering

CCR's software engineering group applies a disciplined approach to the development and maintenance of computer software to facilitate faculty led research. The group supports a wide variety of scientific disciplines on a number of development platforms (including Linux, PC, Web-based software) and maintains expertise in a number of programming languages including C, C++, Java, PHP, Perl, and Fortran, among others. Expertise includes all aspects of software engineering including software stakeholder identification, generation of software requirements, design and implementation of code, testing, and iterative design. In addition, CCR supports machine architecture design, algorithm development and optimization, database engineering, GUI interface design, security, web portal design.

Examples include:

  • REDfly, a collection of known Drosophila transcriptional cis-regulatory modules
  • Genotator, A dynamic and customizable microbial genome annotation system for publishing and editing bacterial and viral genomes.
  • The AAHSL library statistics portal, developed for the Association of Academic Health Sciences Library to support the collection, analysis, and presentation of annual statistical information for libraries in the United States and Canada.
  • UBMoD (UB Metrics on Demand), an open source data warehouse and web portal for mining statistical data from resource managers (TORQUE and OpenPBS) commonly found in high-performance computing environments.

 

Scientific and Medical Visualization

Development of custom, easy to use 2D and 3D visualization applications complete with graphical user interfaces (GUI's) for scientific and medical visualization applications. Expertise in widely used visualization tool kits such as VTK, FLTK, OpenSceneGraph, and OpenGL, as well as extensive expertise in the 3D reconstruction of 2D medical imaging data, including CT, MRI, PET and SPECT imaging. We are capable of visualizing many time varying scientific data sets, including but not limited to: molecular simulations, chemical reactions, and other complex systems.

Scientific and Medical Visualization Projects

 

Bioinformatics

Bioinformatics resources at CCR currently provide users with access to two enterprise level genomics packages and software for DNA and protein sequence analysis, database search, gene expression analysis, biological pathway analysis, statistical computing, and inferring phylogenies. Other support includes the development of customized software tools to support faculty led research (Perl programs, GUI interfaces, database design and schema, web based portals development, etc), advanced data analysis, mining for research projects and funding application.

 

Advanced Database Design and Data Mining

CCR provides advanced database support including customized database schema design, import and normalization of data, query optimization, data warehousing, database server specification, custom web-based access to hosted data, and hosting & administration. Current installations include multiple MySQL and Oracle databases containing billions of rows of data totaling over 3 terabytes of data.

Examples include:

AAHSL Stastical Analysis Portal

REDfly

Tops Markets Purchasing Research

 

Urban Simulation and Modeling and Computer Animation

CCR's Urban Simulation and Visualization team has extensive experience and knowledge working with real-time (interactive) visualization, animation, and all of the mostly widely used animation/simulation packages, including Visualization Toolkit, Multigen-Paradigm Creator and Vega, 3DStudioMax, Alias|Wavefront Maya, SGI Performer, OpenSceneGraph, and Adobe Photoshop. In addition to using these standard commercial software packages, CCR's Urban Simulation and Visualization Team has developed several of its own custom packages and development tools. Most noteworthy is a package called TrafficSim3D, an OpenSceneGraph based package which takes the output of traditional traffic simulation packages and displays it in an interactive (real-time) 3-D environment. Applications include Urban Design and Planning, and Transportation Engineering.

CCR staff have worked on several high profile projects for agencies such as the Peace Bridge Authority, the City of Buffalo, the New York State Thruway Authority, and the New York State Department of Transportation. They have also completed projects for local and multi-national consortiums, such as the Buffalo-Niagara Medical Campus Project, the Cars Sharing Main Street Project, and the International Peace Bridge Project. They have also worked on music video animations for MTV2's Video Mods series.

Urban Visualization Projects

Animation Projects

 

Cluster Management

The staff at CCR has developed extensive experience designing, building, and maintaining Linux based clusters consisting of tens to thousands of processors. This includes all aspects of cluster technology, such as high-speed interconnects, advanced networking, storage area networks, parallel file systems, batch queuing software, and fault tolerant services. Currently CCR maintains hardware and software for a wide variety of research areas, including Civil Engineering, Mechanical and Aerospace Engineering, Chemistry, and Physics.