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My Projects
- Sybyl scripts
- Sequence Analysis Tutorial
- Phalanx Interface
- Revision of the BimCore Subscriber Process
Fall Update: 2001
| Things: The interface I started working on this summer is nearing completion - if there is such a thing. The Celera calendar is now asks our subscriber database whether a person is authorized to sign up. Here's a script that will extract our current Celera subscribers. It needs to be run from sleepy. |
Summer Projects: 2001
| Recent Goings-On: Over the summer of 2001, I've worked on various projects
in varying degrees. The first of which was a site re-design. As you can see,
BimCore's new site is now in compliance with the Med School's specifications
and is organized much differently (and more coherently) than BimCore's old site.
I resolved the problems users were experiencing with our Affymetrix machine and its software suite. Apparently, the Microsoft software Affymetrix chose to interface with their suite is incapable of functioning properly unless the user is logged on as an Administrator. So currently all Affymetrix users have full control of the system, which is a bad thing security-wise, but so far we haven't had any problems. There were a few failed projects this summer. One of which was using a database driven content management system using Zope. It was determined that the Zope software did not yet have all the features we required. Considering the recent improvements in Zope's functionality, we still may implement it. Another failed project was the Bionavigator beta test. Entigen's beta C version of their software proved incapable of properly handling the ACD file interface system. There was a problem with the Oracle database not registering updated ACD files. Therefore, the custom interfaces planned for some of our software were put on hold until Entigen could polish the code some more. I wrote an extended web interface for Threader accessible through the cgi-bin. Unfortunately, due to a licensing problem, Threader is no longer running here at BimCore. The author of Threader (and the person responsible for distributing licenses) has been quite busy this summer moving between universities. He has not been able to find the time to re-license any copy of Threader. The webserver was moved from Snowwhite to Sleepy during the site re-design. Also, the pages from Protein9 were added to the new web server on Sleepy. This created *alot* of broken links and has caused many other headaches (due to hardware malfunctions). I fixed all of BimCore's internal links. That meant checking some 20,000 links on BimCore's 5,000 static pages. It wasn't easy. There were some that were broken to begin with and others that were broken during the site move, and some that got broken twice! Currently, I'm working on an interface using PHP and an SQL database to manage BimCore's subscribers and their accounts. Once put into place, Kim will be able to activate and deactivate accounts or individual users, keep tabs on billings and consulting hours, and search for users by name, department, or affiliation. The database is designed to be flexible, so having a login for BimCore's site is a future possibility. The other implication of using PHP and SQL is that BimCore's site would have the ability to generate dynamic pages. This would mean easier updates, better link checking, and a more customized experience. |
Sybyl Scripts
| About: In order to get these scripts to work, you must first start up Sybyl.
Once Sybyl is running, from the command console, type "take script.spl" (e.g. "take SuperFast.spl").
Filenames are case sensitive, so you must use the proper case for taking the scripts.
To run the script, just type in the script name with appropriate arguments. Most of these scripts need any .pdbs required for operation to be in the directory you started Sybyl in. If the .pdb is not there, the script will probably crash. |
| Script Name: | Made For: | Description |
| SuperFast | Kim Gernert | Comment: Created for the Parkin Tutorial, this script fits the known .pdbs that were used in creating
a structure of an unknown sequence (using composer). It then writes them into
a MOL2 file. Usage: "superfast name_of_run pdb_filename output_filename" |
| fastselect | William Thiel | Comment: This script creates a static set of residues 143 - 177
in 1ce4. Usage: None. Just run it. |
| hivfit | William Thiel | Comment: This script was designed for 1ce4. It superimposes a number
of 1ce4's structures together. Usage: "hivfit pdb_identifier first_structure last_structure" |
| hivfitadv | William Thiel | Comment: This script is a more advanced version of hivfit.
It gives you a few more options. Usage: "hivfitadv pdb_identifier still_structure first_structure last_structure" |
Sequence Analysis Tutorial
| About: I made a completely new format for the sequence analysis tutorial here. Hopefully, any new material we publish can be assimilated into this format with as little accomodation as possible. |
Phalanx Interface
| About: I made a web interface for the Phalanx program. The interface implements all of features of Phalanx, but since Phalanx was just recently revised, the current interface is not completely up to date. I will be updating the page when the new version is finalized. |
New Subscription Page
| About: I recently updated the subscription page to accomodate more information about BimCore's subscribers. I am also working on creating a viewable database and an area to manage those entries. |
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