User:Markh

From Glabwiki

Link title=Mark Holmes=

Software Developer and Systems Administrator in the lab of Morgan Giddings, at bioinfo.unc.edu. You can mail me at markh at unc.edu.

I began working with Morgan in 2000 at the Eccles Institute of Human Genetics at The University of Utah, when she began planning for a tenure track position. In 2002 we moved to UNC. We developed PROCLAME (PROtein CLeavage And Modification Engine), for using intact protein masses to predict proteolytic cleavages and post-translational modifications. That software, at proclame.unc.edu, continues its improvement with recent open-source licensing, the release of a standalone pure-Java app that will run on all major platforms, and the ongoing PhD work of Stuart Jeffreys to revamp the app.

{ /* Geek warning */ } I also manage the lab's high-performance compute cluster, consisting of ~50 dual-CPU Apple Xserves, two Class C subnets, a Fibre Channel fabric, a storage area network served by an Xserve RAID, and some HPC job management software. Cool toys, if not occasionally frustrating. { /* Geek warning off */ }

I also serve as the lab's resident art historian and Chief Leisure Officer, emeritus.

A few publications

  • Mark R. Holmes, Kevin Ramkissoon and Morgan C. Giddings, Proteomics and Protein Identification, in "Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Third Edition", Edited by Andreas D. Baxevanis and B. F. Francis Ouellette, 2005. Hoboken, NJ: John Wiley & Sons. ISBN: 0-471-47878-4. See wiley.com/bioinformatics, and throw your money down for this beautiful book at Amazon (We get no royalties: it's really a good book).
  • Wisz, M.S., Suarez, M.K., Holmes, M.R., and Giddings, M.C., GFSWeb: a web tool for genome-based identification of proteins from mass spectrometric samples. J Proteome Res, 2004. 3(6): p. 1292-5. Summary.
  • Holmes, M.R. and Giddings, M.C., Prediction of posttranslational modifications using intact-protein mass spectrometric data. Anal Chem, 2004. 76(2): p. 276-82. PubMed Abstract.

In past lives I have been (in no particular order)

  • Groundskeeper and Work Scholar at the Esalen Institute, birthplace of the Human Potential movement. [pun intended]. Along Big Sur, the steepest meeting of land and sea in North America, Esalen has 13 microclimates in 27 acres. With canyons, huge cliffs, and hot springs, it's some of the most challenging, beautiful, humbling landscape a groundskeeper could ever hope to attend. Also, you and your brother can die if you haven't harnessed in with the right knots while you're working together 200 ft. above the crashing surf.
  • Disc Jockey in the late 70s for Disco On Wheels. We had milk cartons full of vinyl, the proverbial Chevy van, and a sound system to rock the walls, literally. There are fewer sweet feelings in life than vibrating the hardwood floor of, say, the Landover, MD High School Gym, with a 24-channel mixing board at 300 watts per channel, two fine turntables and some Wild Cherry and Parliament.

At the Smithsonian Institution:

  • Intern, Dept. of Mineral Sciences, at the NMNH. Catalogued, handled, sometimes even touched rocks from Antarctica to the Moon. Held the world's largest gold nugget (not on public display for insurance purposes, and bloody heavy). Lots of cataloging and learning about rocks that might otherwise look boring.

Unt ja, a short-order cook, busperson, dishwasher and pizza-thrower – I've washed over a million dishes and cooked thousands of pizzas – bartender and even a waiter (what, you want fries too?!). Also, I was subjected to the lab's first Public Shaming for not bringing meeting-snax, but SuSu has since taken this position.

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