Programming and Web-Design

I program websites, from simple HTML hacks to full-blown Javascript web-apps. I believe in minimalist design, creating elegant UI's for messy real-world data. To build these websites, I've used Drupal, Word Press, Movable Type, Textpattern (on my blog) as well as coding from scratch:

• Jolecule - a web-based viewer of proteins and DNA.
• Pax Americana - a hipster literary journal based in Brooklyn, NYC.
• Jennifer Hale Photography - a photography website.
• Annotatr - a mashup for commenting on academic articles.
• Independent Arts and Media - a community site for an SF arts non-profit.
• News Buffet - an article aggregator for the NY Times.

I've worked as a scientific programmer, and I am comfortable programming in Python, Javascript, HTML/CSS, C/C++ and Fortran at a pinch. Also, I think that D is über cool. These are some of the software that I have written:

• Jolecule - a web-based viewer of proteins and DNA (Javascript).
• Ramachandran Plot Explorer - a highly interactive cross-platform protein viewer (C++).
• Rotamerically Induced Perturbation - accelerated molecular dynamics (Python).
• Hollow - illustration software for proteins (Python).

Computational Structural Biology

I've studied the fundamental structure of protein molecules, from the stereochemistry of the β-sheet to the protein backbone (Ramachandran plot). With Vageli Coutsias, I developed a really neat analytical solution of proline-ring closure. I have also studied the protein folding problem, and can report to you that it is very hard.

I developed new methods in Molecular Dynamics Simulations that probe the local flexibility of protein structures, and generate a wide range of large conformational changes.

I specialize in protein visualization. I wrote a protein viewer (Ramachandran Plot Explorer) dedicated to the manipulation of the protein backbone. With Franz Gruswitz, I developed a useful method (Hollow) of generating clean images of protein channels and cavities. I recently built a protein viewer (Jolecule) for web-browsers using bleeding-edge HTML5 techniques.

I did my research in these labs:

• 2011-present, Bioinformatician, Ian Smith, Monash University, Melbourne.
• 2010, Visiting Research Associate, Michael Lappe, Max Plank Institute, Berlin.
• 2006-2009, Postdoc, David Agard, University of California, San Francisco.
• 2004-2005, Postdoc, Ken Dill , University of California, San Francisco.
• 2002-2003, Postdoc, Robert Brasseur, FSAGx (Gembloux), Belgium.
• 1997-2001, PhD, Paul Curmi, University Of New South Wales, Sydney.
• 1992-1996, BSc, University of New South Wales, Sydney

I've published my research in these peer-reviewed papers:

11. An improved strategy for generating forces in steered molecular dynamics: the mechanical unfolding of titin, e2lip3 and ubiquitin (2010)
    Bosco K. Ho and David A. Agard
    PLoS ONE 5(9):e13068 [pdf|link].
10. Unfolding Simulations Reveal the Mechanism of Extreme Unfolding Cooperativity in the Kinetically Stable α-Lytic Protease (2010)
    Neema L. Salimi, Bosco K. Ho and David A. Agard
    PLOS Computational Biology 6(2):e10000689 [pdf|link]
9. Conserved Tertiary Couplings Stabilize Elements in the PDZ fold, leading to Characteristic Patterns of Domain Conformational Flexibility (2010)
   Bosco K. Ho and David A. Agard
   Protein Science 19:398-411 [pdf|link]
8. Probing the Flexibility of Large Conformational Changes in Protein Structures through Local Perturbations (2009)
   Bosco K. Ho and David A. Agard
   PLOS Computational Biology 5(4): e1000343 [pdf|link]
7. HOLLOW: Generating Accurate Representations of Channel and Interior Surfaces in Molecular Structures (2008)
   Bosco K. Ho and Franz Gruswitz
   BMC Structural Biology 8:49 [pdf|link]
6. Identification of new, well-populated amino-acid sidechain rotamers involving hydroxyl-hydrogen atoms and sulfhydryl-hydrogen atoms (2008)
   Bosco K. Ho and David A Agard
   BMC Structural Biology 8:41 [pdf|link]
5. Folding Very Short Peptides Using Molecular Dynamics (2006)
   Bosco K. Ho and Ken A. Dill
   PLoS Computational Biology 2:e27 [pdf|link]
4. The Ramachandran plots of glycine and pre-proline (2005)
   Bosco K. Ho and Robert Brasseur
   BMC Structural Biology 5:14 [pdf|link]
3. The flexibility in the proline ring couples to the protein backbone (2005)
   Bosco K. Ho, Evangelos A. Coutsias, Chaok Seok and Ken A. Dill
   Protein Science 14:1011 [pdf|pubmed]
2. Revisiting the Ramachandran plot: hard-sphere repulsion, electrostatics, and H-bonding in the α-helix (2003)
   Bosco K. Ho, Annick Thomas and Robert Brasseur
   Protein Science 12:2508 [pdf|pubmed]
1. Twist and shear in β-sheets and β-ribbons (2002)
   Bosco K. Ho, and P. M. G. Curmi
   Journal of Molecular Biology 317:291 [pdf|pubmed]