spencer.bliven.us
Protein words – Spencer Bliven
https://spencer.bliven.us/index.php/2016/12/07/protein-words
December 7, 2016. In my post about creating a DNA font. I mentioned the idea of doing a similar thing for proteins. There are 20 standard amino acids, each with a single character abbreviation. When combined with symbols for ambiguous residues, any combination of letters can be interpreted as a polypeptide, or vice versa. While I haven’t made a peptide font (although Kristian Rother’s Twenty Characters. Would make a beautiful font), I have been playing around with what structures various words would make.
spencer.bliven.us
Regiomeeting at Mont Sainte-Odile – Spencer Bliven
https://spencer.bliven.us/index.php/2014/10/01/regiomeeting-at-mont-sainte-odile
Regiomeeting at Mont Sainte-Odile. October 1, 2014. Panaramic view from the castle ruins. Last week I attended the Rhine-Knee Regional Meeting on Biocrystallography. I gave a talk about CE-Symm. Slides are available as usual on slideshare. But this time I also created a lecture cast on scivee. I couldn’t figure out how to edit the presentation, so the audio includes a bit of the previous speaker. Me posing with the Heidamür. The hiking group at Dreistein castle (at least those not scared of heights).
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Castle Panic pieces – Spencer Bliven
https://spencer.bliven.us/index.php/2013/08/28/castle-panic-pieces
August 28, 2013. I’m quite proud of my recently-released Castle Panic game pieces. Castle Panic is a great game, and it is fun to have some sturdy walls and towers to replace the flimsy cardboard ones it comes with. I spent a long time figuring out how to use Sketchup for the 3D models and figuring out how to get my printer to make good-looking bricks. The design is CC-BY, and can be downloaded from thingiverse. Leave a Reply Cancel reply. Your email address will not be published. Using BioJava from R.
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New publication on CE-Symm – Spencer Bliven
https://spencer.bliven.us/index.php/2014/04/25/new-publication-on-ce-symm
New publication on CE-Symm. April 25, 2014. Clockwise from left) Symmetry in 1HIV, d2j5aa1, SCOP: d1u6dx , 4DOU, and d1vyma1. My latest paper with Douglas, Peter, Zaid, Andreas, Philippe, and Phil is out! Douglas Myers-Turnbull, Spencer E. Bliven, Peter W. Rose, Zaid K. Aziz, Philippe Youkharibache, Philip E. Bourne, Andreas Prlić, Systematic Detection of Internal Symmetry in Proteins Using CE-Symm. Journal of Molecular Biology. Open-access, etc, so try it out. On your own protein structure.
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A PDB-wide, evolution-based assessment of protein–protein interfaces – Spencer Bliven
https://spencer.bliven.us/index.php/2014/10/21/a-pdb-wide-evolution-based-assessment-of-protein-protein-interfaces
A PDB-wide, evolution-based assessment of protein protein interfaces. October 21, 2014. My first paper in collaboration with the Capitani team has been published online:. Kumaran Baskaran, Jose M Duarte, Nikhil Biyani, Spencer Bliven and Guido Capitani. (2014). A PDB-wide, evolution-based assessment of protein protein interfaces. 14:22 doi: 10.1186/s12900-014-0022-0. It’s been really rewarding working with the team at PSI this year, and it’s great to see our work come to fruition! Structures and interfac...
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spencer – Spencer Bliven
https://spencer.bliven.us/index.php/author/spencer
December 7, 2016. In my post about creating a DNA font, I mentioned the idea of doing a similar thing for proteins. There are 20 standard amino acids, each with a single character abbreviation. When combined with symbo. April 13, 2015. Our latest paper on the CE-CP method for finding protein circular permutations is in this month’s issue of Bioinformatics. Spencer E. Bliven, Philip E. Bourne, and Andreas Prlić. (2015) Detecti. Using BioJava from R. April 10, 2015. October 21, 2014. October 1, 2014. I lea...
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TV Oscilloscope Part 2 – Spencer Bliven
https://spencer.bliven.us/index.php/2013/01/16/tv-oscilloscope-part-2
TV Oscilloscope Part 2. January 16, 2013. To further test out my TV oscilloscope. I hooked it up to the output from a small stereo. Changes in dynamics and instrumentation were very apparent in the songs I listened to. I find the blue start and red tail of the trace to be interesting (clearest in the upper right image). Perhaps the red phosphors energize slightly faster, while the blue phosphors persist slightly longer? 2 thoughts on “ TV Oscilloscope Part 2. February 11, 2013. May 3, 2015. A PDB-wide, e...
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Connections – Spencer Bliven
https://spencer.bliven.us/index.php/connections
Although I plan to keep this page reasonably professional, there are a few of my residences on the Street. Which may prove relevant. If you’re looking for dirt on my personal life these may or may not help. A stream of my thoughts. Here are some sites and resources that I’ve enjoyed or found useful. On the PDB website. Most code was written by Andreas Prlić. With some of the jCE Circular Permuations algorithm by myself. Provides a detailed and informative discussion of Washington weather.
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WordPress with Sqlite on PHP 5.1 – Spencer Bliven
https://spencer.bliven.us/index.php/2010/11/12/wordpress-with-sqlite-on-php-5-1
WordPress with Sqlite on PHP 5.1. November 12, 2010. After a long plod, I finally got wordpress running on acsweb! This is exciting, since it means it is possible to comment on posts, link to them, google for them, etc. Setting up wordpress was made challenging at every turn by my crappy UCSD server, which is outdated or badly configured in a number of respects:. No MySQL, so I had to use the PDO plugin. With a Sqlite database. PDO for WordPress. Copy all the contents of the zip file into. Look at your w...
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The Statistics of Monopoly – Spencer Bliven
https://spencer.bliven.us/index.php/2012/02/22/the-statistics-of-monopoly
The Statistics of Monopoly. February 22, 2012. American Edition Monopoly board. (Source: wikipedia. Armed with a college-level understanding of statistics, I thought I would test my childhood hypothesis that the probability of landing on St. Charles is higher than for other properties. The movement aspect of Monopoly can be modeled as a. Mathbf{x} t = left[ 1, 0, 0, dots, 0right].$. With a peak 7 squares forward. For instance, the probability of moving to each square if you were previously on GO! We can ...
