PMID Classifier

1.      Open PuTTy on the desktop

2.      The host and port have been saved but they are:

a.       Host: classifier.internal.iedb.org

b.      Port: 30022

c.       Connection Type: ssh

3.      After entering 2a – 2c, click “Open.”

4.      You will be prompted for a login as (rohini) and password (classify!123).  Hit “enter” after typing each of them.  You can see characters for the username but the password will be invisible.

5.      Change directory using cd /srv/www/classifier_tool and hit “enter”

6.      Open the browser and type the address as http://classifier.internal.iedb.org:8080/classifier_tool/ and hit “enter”

a.       It will tell you it cannot find the server but it needs to be open for (7) to work

7.      To run the tool, type: python manage.py runserver classifier.internal.iedb.org:8080 into the PuTTy screen and hit “enter.”

8.      You will need to select “Try Again” on the browser page to connect to the opened site.

9.      Use the options given on the opened site to run the tool.

10.  Once the classifier is run, a link will appear from which the results can be downloaded. (Emily knows all these things).

a.       Click on the link and open the zip file.

b.      Drag the files to the query folders. 

PDB Classifier

The PDB query is run on Rohini’s computer.

1.      The query and other files are located on Rohini’s computer and placed into Places à Home Folderà bcell_textclassifierà iedb_files but there is a shortcut to iedb_files on Rohini’s desktop. 

a.       Open the iedb_files folder.

b.      Do not touch any of the lone text files (“ann results”). 

c.       The folder called “Initial catch up run for classifier” has the 7/31/12 files, which were the set of files generated after the PDB classifier was run for the first time.

2.      Open the Terminal, which is located on the taskbar.

a.       Type cd bcell_textclassifier/ [enter]

b.      Type ./runClassifier.sh [enter]

                                                  i.      Once you type [enter] you will see script.

                                                ii.      When the query is finished, the Terminal script text says “see folder iedb_files for results.”  The next line says “rohini@...”.

                                              iii.      When the script is finished running you can close the Terminal.

3.      When the script has finished running, go to the iedb_files folder

a.       If there are new PMIDs the date at the end of ann_results_pmid_2012-7-31 will be renamed with the day you ran the query and you will also see a zip file dated with the day you ran the query.  Here, “2012-7-31” is the day the query was last run and would be replaced with 2012-8-6 if there were new PMIDs on 8/6/2012.

b.      The output will be in a zip file (locate zip file icon in iedb_files folder called “ann_results_pmid_2012-7-31.zip” [or whatever the date run was]).

c.        Take the zip file and put it on the desktop.  Open the files from the desktop and send the files to your e-mail.

d.      Delete the zip file after but make sure the files you sent to yourself are correct.

4.      If new PMIDs were not found, the date at the end of the files will not be updated.