4 ms·

Any clue what software/technology they are using? I'm guessing Java.

by Cieplak 14y ago

tosseraccount 14y ago
It appears to be hodgepodge of technologies but mostly Matlab (.m) ... Downloaded code zip file and unziped to to "WholeCell" directory find WholeCell -type f | awk '{FS="."; print $NF}' | sort | uniq -c | sort -n ... 2 java 2 lib 2 log 2 mexa64 2 mexw32 2 pdf 2 swf 2 vbs 2 xlsx 3 exe 3 fsa 3 mexw64 4 jpg 4 svg 5 desktop 5 license 5 sql 5 TXT 6 col 6 sh 6 tmpl 6 tpl 7 ico 7 xml 8 bat 8 pl 8 z 9 json 15 dot 16 gif 18 map 19 css 23 dll 24 dat 25 p 52 mat 62 txt 114 jar 238 png 277 js 427 php 531 m 1096 html
- apl 14y ago
  A lot of that stuff is incidental stuff; see .php, .html, .js, and so on. (Apparently there are some web-based tools that he mentions; not sure, though.) The bulk amounts to MATLAB plus Java libraries for remedying MATLAB's functionality gaps.
dglassan 14y ago
I'm wondering the same thing
apl 14y ago
Nope. Seems to be heavily MATLAB-based.
kibwen 14y ago
I know exactly zilch about this field, so it very well could be something that mundane. However, for spreading calculations across a cluster of 128 computers, I sort of hope they're using something more specifically tailored for the task. Keeping in mind that my knowledge is zilch, here are some exotic languages that appear to be designed for this sort of thing: http://en.wikipedia.org/wiki/X10_%28programming_language%29 http://en.wikipedia.org/wiki/X10_%28programming_language%29 http://en.wikipedia.org/wiki/Chapel_%28programming_language%29 http://en.wikipedia.org/wiki/Chapel_%28programming_language%... http://en.wikipedia.org/wiki/Fortress_%28programming_language%29 http://en.wikipedia.org/wiki/Fortress_%28programming_languag...
bugsbunnyak 14y ago
The source code is available. https://simtk.org/project/xml/downloads.xml?group_id=714#package_id1169 https://simtk.org/project/xml/downloads.xml?group_id=714#pac... I went to a talk by Dr. Covert a few months ago and it was fascinating, all the moreso as a chalk-talk with an animation flip-book handout. As an aside, since the topic of CS folks helping with biology research comes up often: apparently a Google engineer went on sabbatical to the Covert lab and helped re-architect and optimize the system to the point that it was feasible for this research. There are many other projects that would benefit from this type of expertise.
jkarr 14y ago
We used MATLAB. We organized the training data into a database (referred to as the "knowledge base") which was implemented in MYSQL with a web-based UI implemented in PHP. The various other scripts in shell and Perl were used to run the model on our Linux cluster.

Any clue what software/technology they are using? I'm guessing Java.

by Cieplak 14y ago

Any clue what software/technology they are using? I'm guessing Java.

It appears to be hodgepodge of technologies but mostly Matlab (.m) ... Downloaded code zip file and unziped to to "WholeCell" directory find WholeCell -type f | awk '{FS="."; print $NF}' | sort | uniq -c | sort -n ... 2 java 2 lib 2 log 2 mexa64 2 mexw32 2 pdf 2 swf 2 vbs 2 xlsx 3 exe 3 fsa 3 mexw64 4 jpg 4 svg 5 desktop 5 license 5 sql 5 TXT 6 col 6 sh 6 tmpl 6 tpl 7 ico 7 xml 8 bat 8 pl 8 z 9 json 15 dot 16 gif 18 map 19 css 23 dll 24 dat 25 p 52 mat 62 txt 114 jar 238 png 277 js 427 php 531 m 1096 html

apl 14y ago
A lot of that stuff is incidental stuff; see .php, .html, .js, and so on. (Apparently there are some web-based tools that he mentions; not sure, though.) The bulk amounts to MATLAB plus Java libraries for remedying MATLAB's functionality gaps.

dglassan 14y ago

I'm wondering the same thing

apl 14y ago

Nope. Seems to be heavily MATLAB-based.

kibwen 14y ago

I know exactly zilch about this field, so it very well could be something that mundane. However, for spreading calculations across a cluster of 128 computers, I sort of hope they're using something more specifically tailored for the task. Keeping in mind that my knowledge is zilch, here are some exotic languages that appear to be designed for this sort of thing: http://en.wikipedia.org/wiki/X10_%28programming_language%29 http://en.wikipedia.org/wiki/X10_%28programming_language%29 http://en.wikipedia.org/wiki/Chapel_%28programming_language%29 http://en.wikipedia.org/wiki/Chapel_%28programming_language%... http://en.wikipedia.org/wiki/Fortress_%28programming_language%29 http://en.wikipedia.org/wiki/Fortress_%28programming_languag...

bugsbunnyak 14y ago

The source code is available. https://simtk.org/project/xml/downloads.xml?group_id=714#package_id1169 https://simtk.org/project/xml/downloads.xml?group_id=714#pac... I went to a talk by Dr. Covert a few months ago and it was fascinating, all the moreso as a chalk-talk with an animation flip-book handout. As an aside, since the topic of CS folks helping with biology research comes up often: apparently a Google engineer went on sabbatical to the Covert lab and helped re-architect and optimize the system to the point that it was feasible for this research. There are many other projects that would benefit from this type of expertise.

jkarr 14y ago

We used MATLAB. We organized the training data into a database (referred to as the "knowledge base") which was implemented in MYSQL with a web-based UI implemented in PHP. The various other scripts in shell and Perl were used to run the model on our Linux cluster.