I provide direction to the ProSight development team, and provide bioinformatic support to the Proteomic Center of Excellence.

I am the manager for the National Center for Genome Analysis Support at Indiana University.The National Center for Genome Analysis Support is an NSF funded resource designed to supply bioinformatic support and computational infrastructure to genomics projects requiring large RAM computational resources – specifically de novo sequence assembly. We provide consulting services for biologists, assistance in running genome analysis software, hardened and optimized genome analysis software, and an equitable and easy to use allocations process for accessing our large-memory computational cluster. Our cluster, Mason, is a 16 node system with each node having four Intel Xeon L7555 8-core processors and 512 GB of RAM. Thus Mason has a total of 512 processors and 8 TB of RAM. We have a variety of additional high-performance computing skills and assets that can be applied to genome analysis projects. If you have received NSF funding for your genomics research, we can provide these services to assist that research. If you are submitting a grant to NSF, NCGAS can also provide a letter of support for your project, and we are happy to discuss partnership arrangements as well.

Provided bioinformatics support on several research areas including pathway visualization, proteomics project coordination and design, and assisting the software development team in designing and implementing a general purpose data storage system in Ruby on RAILS. Provided bioinformatics consultation and support for GLBRC researchers including ad hoc analyses of next-generation sequencing, proteomic, and bacterial growth results in SAS, Perl and R. Developed novel metabolic pathway visualization system in Cytoscape and R for displaying complex multiomic experimental results.

Provided bioinformatic support to a mid-sized proteomics core facility within the medical school. Developed and implemented a label-free quantification strategy currently used for approximately two dozen experiments on both human and model organisms. Interacted closely with principle investigators regarding the design and implementation of translational medicine studies. Maintained computer hardware/software/network infrastructure consisting of 12 servers and 92 TB mass storage. Developed novel software and scripting solutions for data management. Provided administrative and/or user support for Matrix Science Mascot, Proteome Software Scaffold 2.x and 3.0 and batch Scaffold, Sorcerer2 (SageN), Rosetta Elucidator including an Oracle 10g backend and other proteomic applications.

Programmer and manager of development for ProSight PTM. Architect and bioinformatician for ProSightPC a stand-alone Windows PC application for the identification and characterization of proteins from top-down mass spectrometry. Supervision a team of graduate and undergraduate student programmers. Development of both GUI-driven targeted data analysis applications and automated high throughput tools. The targeted applications are described in detail in Current Protocols in Bioinformatics Chapter 13, unit 6: LeDuc and Kelleher (2007) Using ProSight PTM and Related Tools for Targeted Protein Identification and Characterization with High Mass Accuracy Tandem MS Data.Additional work included web and database development for an EST management system, various web master projects, and database programming.

Database Programmer: Responsible for the development and implementation of a SAS-based data management system for real-time data collection from several Allen Bradley PLC networks and a Campbell Datalogger network. This task included: 1) the development of an Oracle to SAS cross-platform (UNIX to WinNT) communication system, 2) the implementation of Rockwell Software's RSSQL, and 3) the rewriting of existing C programs, Perl, UNIX Shell and SQL-Plus scripts into SAS and Perl scripts.PalmOS Programmer: Developed and implemented a data collection system for remote field crews. The system used C applications targeted to the PalmOS as a front end, and a MySQL database supported by several Perl and PHP3 scripts as a backend. Also developed specialized calculation software for the PalmOS. Administered two Windows NT servers, and one SunOS 5.0 machine. These machines ran SAS Server (SAS 6.12 and SAS 8.0), Apache, and Oracle 8.