IllinoisTools/4 July 2009

• • • Note: Our notebook is organized in a weekly fashion. Click on the Saturday of every week to view the notes from the previous week.

6/28-7/4

Donny

At this time, I have a working prototype for the site. It has a user interfaces with forms and/or dropdown menus to select the desired compound. From there the site will return the shortest path (by number of reactions). It displayed the KeggID and common name of each intermediate, as well as the reaction ID's that correspond to the returned pathway. It's final feature to date, is listing the cofactors and additional substrates that were assumed to be present for the pathway to succeed.

Kanishka

Biobricks!! - The goal of our project will be to provide the user with all the biobricks that code for all the enzymes needed for a particular reaction pathway. So first, we will have to figure out the genes that code for all the enzymes that will carry out a particular pathway. First, we will take the nucleotide sequences for these genes and check whether the exact sequence already exists in the existing biobrick database. So we will have to scan through the biobrick registry to compare our sequences with the existing sequences. Since the current biobrick registry only has about 3200 parts, it is highly unlikely that the exact sequence will already be existing. However, if any of the sequences do already exist, the program will tell the user that the biobrick for that particular gene already exists, and for the remaining sequences, the program will construct biobricks for all these genes and display them for the user. Now from what I think, each biobrick will be one gene. (Because one enzyme cant come from two different genes, but one gene can code for several proteins). Each gene can either code for a single enzyme, or multiple enzymes. So if a particular reaction pathway contains 20 enzymes, there may be up to 20 different biobricks. The program will add the appropriate suffix and prefix to the sequences, assign them to a biobrick standard, and then present them in a proper biobrick format. (Now Im not sure if we could combine these biobricks into one biobrick, since all the biobricks code for one reaction). So the user then can order all these biobricks, and then in lab, can insert these plasmids into a bacteria and carry out the particular reaction. If we can, we should actually test this out in lab with the help of the wetlab team.

Riyad Worked with Kanishka on biobricks. He pretty much did an excellent job summing it up so not much to add. Right now we are looking into incorporating sometype of BLAST into our program to compare our output gene sequence with the biobrick registry.

Palak

This week I began working on an algorithm that would search for the path with the fewest changes to the host organism. I got the algorithm to function properly but the database did not have all the organisms paired up with the reactions yet. The next steps will be to populate the database with the additional information such as reversibility of reactions and stoichiometry.

Nate

This week I decided to take a break from KEGG, and decided to start working on the look and feel of our wiki page, which was looking pretty sad at this point. While everyone worked on other things, I learned a bit about CSS and HTML, and I drafted a design for our wiki page. By fourth of july weekend, I had our wiki page all set up, with some fun colors; blue and orange background design with orange textboxes....apparently nobody like the color scheme, so I will have to alter the colors later. I also created some graphics for our website as well. The most rewarding achievement this week was being able to make a toolbar/navigation bar for our wiki using CSS. It took me a while to figure it out. In the future I hope to make our website look a little bit more appealing and organized.