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Spencer Bliven
Works at UC San Diego
Lives in San Diego, CA
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Spencer Bliven

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Tweet. I'm a fan of literate programming. When I'm writing a paper, I typically use LaTeX to draft the paper, Java to generate the data, and R to create figures and do basic analysis. With Sweave (or the more recent Knitr package), it is possible to easily add R code to LaTeX documents.
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Spencer Bliven

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Universal Pellet Extruder - Adventures in Granular materials - community project #3dprinting   #RepRap  
Pellets - Let's shake things up! A few months back I asked the question on G+, Would anyone like to discuss Pellet / Granular extruders? I ask because I have been working on various designs for quite some time with success an...
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Wow, a nematode wirehead, living in a virtual world. We feed it false sensory data and let the worm drive its robot body around.
Next step: uploading a human brain into a computer.
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Someone should compile Darwin Prize and BAHFest entries and see if anyone can distinguish them.
The unexpectedly popular BAHFest searches for the year's most laughable evolutionary theory, and rewards its creator
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My post on this year's ISMB conference. Includes links to my slides and poster.
Tweet. I had a great time at the ISMB conference & related events in Boston last week. As always, it is an exciting event scientifically and socially. First there was the Open Bio Foundation's Codefest for contributors to the Bio* libraries and other open source bioinformatics tools.
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These are beautiful.
 
Chemical Calligraphy - DNA Molecule - http://dscript.org/chem.pdf
http://dscript.org/note.pdf  - DScript BioChem and other Notations. All pics, text, pdfs, etc.. free to copy edit sell and use for commercial purposes, no royalty, fee, etc.
Dscript 2D Alphabetical Intro - http://dscript.org/dscript.pdf

Some Short Stories in Dscript : http://dscript.org/story.pdf

Mad Science Inventions & Experiments : http://dscript.org/inventions.pdf

WireScript 3D writing system : http://dscript.org/wirescript.pdf
NailScript Layered writing system : http://dscript.org/nailscript.pdf

Facebook Collection : http://facebook.com/dscripting (Plz Like and share, it's not easy being an artist)
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Spencer Bliven

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Congratulations to the BioJava team ( +Andreas Prlic +Spencer Bliven and many others ) on their latest release BioJava 4.0.

New Features:

General
• Consistent error logging. SLF4J is used for logging and provides adaptors for all major logging implementations. (many contributors, including @benjamintboyle and @josemduarte)
• Improved handling of exceptions (@dmyersturnbull)
• Removed deprecated methods
• Expanded the BioJava tutorial (@andreasprlic, @josemduarte, and @sbliven)
• Updated dependencies where applicable
• Available on Maven Central (@andreasprlic and @heuermh)

biojava3-core
Improved Genbank parser, including support for feature records, qualifiers, and nested locations. (@paolopavan and @jgrzebyta)

biojava3-structure
• Better support for crystallographic information, including crystallographic operators, unit cells, and protein-protein interfaces. (@josemduarte)
• Better organization of downloaded structure files (set using the PDB_DIR and PDB_CACHE_DIR environmental variables) (@sbliven)
Better command-line tools for structure alignment (@sbliven)
• New algorithm for symmetry detection in biological assemblies (@pwrose)
• New algorithm for fast contact calculation, both intra-chain and inter-chain (@josemduarte)
• Support for Accessible Surface Area (ASA) calculation through and implementation of the Shrake & Rupley algorithm, both single-thread and parallel (memory permitting) (@josemduarte)
• Support for large structures (memory permitting) and multi-character chain IDs.
• Default to mmCIF file format, as recommended by the wwPDB

This version is compatible with Java 6, 7, and 8.
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The Personal Genome Project is looking for San Diego volunteers to be sequenced. I would totally participate if I were in town.
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Trippy interactive fractal
Project information and source code is released under GPL version 2 or higher. When applicable, all other project information is released under Attribution Non- Commercial Share- Alike 3.0 license. All original writing and artwork is © on the date of posting to the original post author.
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Impactstory will start charging $60/year for their service. Here's an interesting defense of the move. The best quote:

"Would you still use a free service if it costs $5/month? If the answer is no, it’s most likely a waste of time and you should not use it even if it is free."

Sadly, I'm not sure that Impactstory has demonstrated that it's worth the cost. I know they're trying to add new features, but for me it's still primarily an aggregation service.
Last week Impactstory announced their new paid subscription model. Changing a service from free to paid is a big step and there was some discussion on Twitter about it. We decided from day one to run Paperpile as a paid subscription service and only had good experiences with this model so far. We are lucky toRead more...
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Matthew, what's how does your writing speed compare using Dscript vs. Latin characters for English? Do you think it could be viable for note taking (like shorthand, for instance), or do you think its strength is the artistic/2D aspects?

In experimenting with the script I felt like I was thinking a lot about composition and layout, rather than just remembering the glyphs. With more practice does one figure out the rules for the ligatures, or do you continue to have to think about the various options and how they will influence the overall aesthetics?

I love the art, especially the kaleidoscope-type pieces.
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well as per ornamental version, i think all languages have that too. English Gothic script, for example, is quite ornamental

As per reading others writing. there is a definitely some effects there. similar to the way there are so many handwriting style elements that you might find it hard to read someone elses cursive or quick written notes.

how this effect differes between say Dscript and standard latin script is another issue I have not studied nearly enough.

I would say it is safe to assume there are 2 primary aspects to look at
1)the complex merging of Dscript letters are flexible but there are clear rules as to how all details hold some value.  This brings increased density of information and the overall shape becomes more "volatile"
2)latin script is often megred and combined to save penstrokes and time, but when it does it relies on a visual shape based reading, where extra details/connection are meant to be ignored (sometimes people connect letter in cursive ways that have no real rules except "preserve the overall shape")

So.. which is harder to read.. regulated combination methodology without shape preservation? or shape preservation with less regulated combination methodology?

I would guess it is analogous to computer data compression

There is always a trade off between "processing power for decompression" and "data compression"

Dscript uses less pen strokes, lifts and overall requires less 2D detail on average... one could say "the data has been compressed more"

But the trade off is that the computer(or human brain) must "think" more in order to decompress the data

That all being said, human have a VERY strong affinity for symbols and glyphs (traffic signs, @ .&, #, etc..) so it is possible is Dscript were ever "standardized" so that 1 form per word were assigned (this would free up other forms to carry separate meaning... one form of "die" might mean "english: death" and another "german: the")

Assuming it could be standardized.. then it is possible.. assuming human have a natural affinity for symbols and glyphs.. that Dscript could prove to have faster reading than standard latin alphabet.. if it were compared "native Dscript" vs. "native Latin Script"... but there is no one on earth who is "native Dscript" so this is hard to test hehe

on the note of compression, if you have not seen Cscript, it is another approach to compressing the data.. but in a computer friendly way (Dscript OCR is much more processor intensive than latin script... Cscript OCR requires much less processing than latin script)

So happy you like :) its a fun puzzle game at tthe very least :) if you ever have question or comments, always love to chat :)
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Tweet. I learned some interesting facts about fetal development recently. So interesting, they can only be properly delivered by Doctor McNinja (using the awesome Dinosaur Comic mashup template) McNinja is developing a novel treatment for patent ductus arteriosus using Gordito's mustache.
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In his circles
100 people
Have him in circles
120 people
Jonathan Wright's profile photo
Christopher DeBoever's profile photo
Gonzalo Parra's profile photo
Shai Oren's profile photo
Manrico Genoni's profile photo
Douglas Myers-Turnbull's profile photo
Joris Vankerschaver's profile photo
othniel zokou's profile photo
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Bioinformatics PhD student at UCSD
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Bellevue, WA - Zurich, Switzerland - Seattle, WA
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