Patrick's BIMCORE Projects

[ programming - tutorials - research - chime - mage - miscallaneous - others' tutorials ]

In the area of programming...  [ back to top ]

Web Tools

Command Line Tools

I wrote a cgi interface to use ALL the features of probe on the web I wrote a cgi program to convert your pdb file into its one letter abbreviated code A molscript cgi page is in the works I updated (and improved I hope) a cgi program for Modeller on the web I have put an initial version of a cgi program for Dock on the web I starting to put Threader on the web and linking it to modeller adapted a web page counter - for us: how to put it on your page Sequence Aligner aligns threader and blocks results back onto the sequence Multiple blast searching and with fetched extrez comparison (help) Lab Scheduler that allows you to schedule time on BIMCORE's computers

a program that converts pdb files to gzipped files run: ~pmcconn/pdb2zip see: source a program that converts gzipped files back to pdb files run: ~pmcconn/zip2pdb see: source a program to give you the hex code for a color given the rgb numbers and vice versa run: ~pmcconn/color see: source Multiplexed primer program run: ~pmcconn/Primer/src/primer see: source a program to replace columns in a pdb file run: ~pmcconn/pe see: source a program to recursively read comments from html files run: ~pmcconn/Data/readcomments see: source

In the area of tutorials...  [ back to top ]

• The permissions for gmb790r have been set on a new page
• If you are a molmod login user, and can't remember how to copy files over to the web server, see this cheet sheet
• Revamping of The Potassium Channel Tutorial with clickable pictures and interesting pseudo-animations
• Tutorial on advanced scripting of chime and javascript-chime interaction
• How to make your tutorials load up all the frames for each link
• Sequence Analysis Tutorial (blast, blocks, prodom, domo)

In the area of research...  [ back to top ]

• Binding in 14-3-3 proteins
• Remodelling of IC140

In the area of Chime...  [ back to top ]

• builder script  builder2 script
• toggle script   toggle2 script   toggle3 script
• atom picker   atom picker2
• floating windows
• zapping chime window on page unload

In the area of Mage...  [ back to top ]

• Magelet applet example
• How to put in a Magelet applet

Other things I have done the summer of '99...  [ back to top ]

• Scanned some of the gmb790r lectures into pdf format
• Backed up and cleaned up hard disks
• see a pop up window on test.html
• amino acid abbreviations
• molecules can be toggled in chime with a little trick and see a zooming demo
• see a demo of a molecule in VRML being clickable
• made a cover for a magazine
• make a link pop up multiple images

Tutorials written by other BIMCORE staff  [ back to top ]

• apolipoprotein E
• Immunoglobulins
• Reverse Transcriptase - I put on first use of the pop-up help window we are incorporating
• Potassium channel - I helped with some of the javascripting
• Protein Tyrosine Phosphatase - I helped on the beginnings of this one
• DNA Polymerase I
• p53 DNA Regulation
• cAMP-dependent protein kinase