Harvard:Biophysics 101/2009/Infrastructure: Difference between revisions
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This is a listing of background information for those interested in Trait-O-Matic | This is a listing of background information for those interested in Trait-O-Matic | ||
==Tasks== | |||
*Text Classification | |||
--I already have MeSH parsed into a mySQL database, I am currently working on ICD-10 as a supplemental hierarchy of diseases [[http://apps.who.int/classifications/apps/icd/icd10online/]]. As soon as this is ready the data will be applied to the classification. | |||
*Reference Extraction | |||
http://incubator.apache.org/pdfbox/ is a Java-based PDF text extractor that we can use to extract paragraphs out from references so that we can then display them together with traits. I will show a demonstration of text extraction in class today! | |||
==Overview== | ==Overview== |
Revision as of 11:07, 12 November 2009
Infrastructure Background
This is a listing of background information for those interested in Trait-O-Matic
Tasks
- Text Classification
--I already have MeSH parsed into a mySQL database, I am currently working on ICD-10 as a supplemental hierarchy of diseases [[1]]. As soon as this is ready the data will be applied to the classification.
- Reference Extraction
http://incubator.apache.org/pdfbox/ is a Java-based PDF text extractor that we can use to extract paragraphs out from references so that we can then display them together with traits. I will show a demonstration of text extraction in class today!
Overview
CodeIgniter Frontend
Database Contents
Revision Control
Joining
- Acquire a Harvard Ethics Training in Human Research (HETHR) certificate by completing the training at [2]. This should take around 2 hours, you have to read 6 of the required sections and 4 of the "electives". Email your certificate to Sasha (awaitz@post.harvard)
- Sign up for access to the control panel at [3]
- Create an RSA ssh public key. This will allow the server to authenticate you. This is done by using the command
ssh-keygen -t rsa
Ensure that your private and public keys are in your .ssh or .openssh directories. Otherwise, ssh will not know where to look for them.
- Upload your public key to the control panel
- Follow the directions on the front page of the control panel. They will tell you to edit your .ssh/config file by adding:
Host *.oxf
ProxyCommand ssh -p2222 turnout@switchyard.oxf.freelogy.org -x -a -o "Compression no" $SSH_PROXY_FLAGS %h
User <YOUR_USERNAME>
- You can now ssh to your node by following the directions on the front page of the contol panel
- To set up trait-o-matic, follow the directions at [4]