1. Fall 2015 Course
  2. Discussion

Discussion

olcc s16 | Thu, 04/06/2017 - 12:12
Dr. Kim, I have cleaned up the Europa orphan drug list as you instructed. However, I might have skipped biological substance while process the original list (which i think it's ok since Pubchem won't give any result from it) and also, I think I catch up some mistake with the drugs nomenclature (such as parenthesis). So, I tried to upload the list into GoogleSheet and linked to CACTUS resolver to retrieve the Standard Inchi Key (but it took forever, and some cell still giving me "loading"). Then, I upload the list to Pubchem as synonyms to find and I got 673 results. I upload to OLCC the original list, the updated, and the list from Pubchem

Cody Ward | Wed, 04/05/2017 - 17:00
This course is the deepest I have ever gotten into programming, so I would say my programming skills are minimal. Being better with Excel, and programs like it, is something I have felt would be very beneficial to me in the future, and this module seemed like a great opportunity to learn something. I am a double major in biology and biochemistry, and I am hoping to pursue optometry school after I graduate. Right now I am helping in a lab that focuses on using microscopy to learn about various processes on the microscopic level. If you have any ideas I would be glad to hear them, since my knowledge of how these sheets can be used is minimal and its hard to imagine what all can be done. Thanks, Cody

Olcc S14 | Wed, 04/05/2017 - 16:18
How can we get the region that shows bioactivity data against histamine receptors from the heat map? I saw there are many GIs and AIDs in the heat map. I am confused what we need to report? Is it GI or AID or CID? Looking forward to your help.

Robert Belford's picture
Robert Belford | Wed, 04/05/2017 - 16:16
Great Cody, I think there is a lot of potential here. Please let Dr. Gupta know, and have her subscribe to comments, as she is the one grading you, and you need to be sure she is happy with what you do. I have a couple of quick questions. Do you have any programming skills? It is not necessary at all, but I am trying to get a bearing. Second, do you have a bearing on what you want to do when you graduate? You should pick a project that helps you, both now, and after you graduate. Module 7 deals with APIs and Dr. Kim is following comments on this module. So my suggestion is that we build up a project off of module 7 that uses PubChem. So what we need, is to figure out what we want our "Smart Spreadsheet" to do. I also will have a student at UALR who can probably work on this too. Cheers, Bob

Cody Ward | Wed, 04/05/2017 - 16:04
Hey, My name is Cody, and I am a student at South Dakota State University. I am interested in this project because I would really like to develop my skills using applications like Excel and Google Sheets. I have been new to many of the things that we have done with google sheets in the previous modules, so I was hoping to learn more of the uses. I was hoping to join this project, and possibly learn a little bit more about how it is going to be done. Thanks, Cody

Sunghwan Kim | Tue, 04/04/2017 - 22:45
For the purpose of homework, I included the limit on covalent unit counts to let students know that the search results can be "filtered or restricted" using various properties. In the homework, the covalent unit count set to 1 does not affect the identity search results, but do affect the similarity search results. In this particular question, the effects of using the covalent unit count limit becomes clearer if you try to run the same similarity search with the covalent unit count set to 2 or larger. This will give you mixture and salt forms that include components that are not likely to be responsible for the bioactivity of the whole records against the target protein.

OLCC S198 | Tue, 04/04/2017 - 20:20
Alright! So, I am planning on using this project opportunity for my chemistry seminar because I have not previously done any chemistry research. Dr. Belford, who is also my seminar mentor, has suggested that my seminar presentation go over how to use Reaxys in finding information for this project since a lot of faculty members attend the presentations and no one knows much about Reaxys. I would like to get started because my seminar is on the 14th of this month. Does anyone have a suggestion about where to begin? Lyndsie

Cody Ward | Mon, 04/03/2017 - 16:44
Hey, I am an undergraduate student from South Dakota State University. I was hoping to learn a little bit more about this project, and quite possibly what I might be doing for the project if I am a part of it. I checked out the WikiData website, and thought it would be an interesting resource to learn more about. Thanks, Cody

OLCC S17 | Mon, 04/03/2017 - 15:02
I don't really understand why we have to limit the number of covalent units while searching for substance. is there any other reason we should do that or is it just the procedure to getting the proper answer? Thanks!