Staphylococcus aureus subsp. aureus USA300_FPR3757

f g x - functional genomics explorer

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Tn mutant library construction and characterization

Dr. Kenneth Bayles of the UNMC Department of Pathology and Microbiology received grant awards from the United States Department of Defense for the construction and laboratory characterization of the NARSA Tn mutant library.

Sanger dideoxy DNA sequencing used to characterize the Tn library was performed by the UNMC DNA Sequencing Core, which is funded in part by grant awards from the NIH's NCRR (1S10RR027754-01, 5P20RR016469, RR018788-08) and the NIH's NIGMS (8P20GM103427, GM103471-09) to the laboratory's director, Dr. James Eudy of the UNMC Department of Genetics, Cell Biology, and Anatomy.

Bioinformatic software development and web site creation

Dr. Robert Boissy of the UNMC Department of Internal Medicine developed the software used for automated Tn insertion mapping, and the SQL Server® databases used for managing DNA sequencing reads, reference genome annotation data, and mapped Tn insertions. Application software was developed using an elegant, versatile, type-safe functional programming language known as F#, an ML-family language that was inspired by OCaml and developed by Dr. Don Syme and colleagues at Microsoft Research. The F# compiler and core libraries are open source, and although F# programs are typically run under the .Net Framework on Microsoft® Windows® operating systems, F# programs can also be run under the open-source Mono Framework on Windows, MacOS or Linux operating systems. There is an F# bindings add-in available for use with the latest version of the open-source MonoDevelop IDE, an F# mode for use with Emacs, and a vibrant community of F# developers. Versions of SQL Server® RDBMS software and intergrated development environment (IDE) software that can be used to create or modify the databases and programs used in this research project are available from Microsoft either free of charge or at exceedingly modest expense via Microsoft’s DreamSpark Academic Program.

Dr. Bayles and Dr. Boissy and their colleagues are currently in the process of drafting manuscripts related to this work. Upon the publication of these papers, all of the source code used in this research will be made available under an open-source license and via a public source-code repository.

This web site was also created using F#, together with WebSharper, an open-source, type-safe, highly productive F#-to-JavaScript compiler and web development framework created by IntelliFactory (Budapest, Hungary). Several HTML5 and JavaScript libraries were also used, and we are very grateful to their developers. A special note of thanks to the developers of the wonderful Krona HTML5 control for visualizing complex hierarchical data! The Krona source code is available here and the Krona publication is available here.

Anton Tayanovskyy and Loïc Denuzière, two exceptionally talented Enterprise Architects from IntelliFactory, created the web site under the direction of IntelliFactory's CEO Adam Granicz and Dr. Boissy, with very helpful feedback and guidance from Dr. Bayles, Dr. Paul Fey, and several members of Dr. Bayles' laboratory (Vijay Yajjala, Todd Widhelm, and Jennifer Endres). Dr. Boissy is responsible for maintaining and improving the site, so any comments, criticisms, and suggestions about this web site or its associated software and databases should be directed to: rboissy [at] unmc [dot] edu.

Major funding for the creation of this web site was provided by a generous grant from Emergent BioSolutions (Rockville, MD, USA).