Home
About Bioinformatics
Bioinformatics or computational biology is the use of techniques from applied mathematics, informatics, statistics, and computer science to solve biological problems. Research in computational biology often overlaps with systems biology. Major research efforts in the field include sequence alignment, gene finding, genome assembly, protein structure alignment, protein structure prediction, prediction of gene expression and protein-protein interactions, and the modeling of evolution. The terms bioinformatics and computational biology are often used interchangeably, although the latter typically focuses on algorithm development and specific computational methods. (In the biology-mathematics-computer science triad, bioinformatics will intimately involve all three components while computational biology will focus on biology and mathematics.) Due to interest from computer scientists and mathematicians and the popularity of computational techniques in the field of genomics, it is commonly referred to as computational biology; a more accurate term is computational genomics. There are also lesser known but equally important areas of computational biochemistry and computational biophysics, that are also a part of computational biology. A common thread in projects in bioinformatics and computational genomics is the use of mathematical tools to extract useful information from noisy data produced by high-throughput biological techniques. (The field of data mining overlaps with computational biology in this regard.) Representative problems in computational biology include the assembly of high-quality DNA sequences from fragmentary "shotgun" DNA sequencing, and the prediction of gene regulation with data from mRNA microarrays or mass spectrometry.
Current Month
 12345
6789101112
13141516171819
20212223242526
2728293031
Jul. 18th, 2008 @ 05:58 pm A little over the top advertising
http://bio-rad.cnpg.com/lsca/videos/ScientistsForBetterPCR/
About this Entry
[info]dr_weir_uk, posting in [info]_scientists_
Jul. 18th, 2008 @ 08:40 am Article request
Can anyone help me with the pdf of this article?

Link

Thank you so much in advance ;)

shylaughter at gmail dot com
About this Entry
[info]choosy_girl, posting in [info]_scientists_
Jul. 17th, 2008 @ 10:09 pm New Website
I've made a website for my TATA box t-shirt: http://tatabox.freeshell.org and you can now email me at tatabox@freeshell.org. It's hosted by the Super Dimension Fortress, which offers free UNIX based hosting.

I will be printing a second batch of shirts, this time with more L's and XL's, that will probably be ready by next week. You can check for updates on my site. Thanks for all your nice comments ! :)
About this Entry
[info]tataboxtees, posting in [info]_scientists_
Jul. 15th, 2008 @ 02:10 pm Article request?
Does anyone have access to this article that they could send to me? Thanks in advance! :)

Class IA phosphatidylinositol 3-kinase: from their biologic implication in human cancers to drug discovery.
Maira SM, Voliva C, Garcia-Echeverria C.
Expert Opin Ther Targets. 2008 Feb;12(2):223-38.
About this Entry
[info]garfpooky, posting in [info]_scientists_
Jul. 15th, 2008 @ 08:51 am (no subject)
I am considering postdocs outside of the US (my country of citizenship). Have any of you guys done postdocs outside your country of origin? What are the pros/cons of this situation? Are there questions I should ask my potential boss to make this process easier?
About this Entry
[info]harleybitch, posting in [info]_scientists_
Jul. 14th, 2008 @ 10:53 pm TATA box shirts
Hi guys,
I posted a couple months ago with my TATA box "I wish I were a DNA helicase so I could unzip your genes" t shirt and some of you guys said you liked and and might be interested in buying it.

So I drew it on Illustrator and printed a few:

The t-shirt design )

How it looks when worn )
About this Entry
[info]cymbelline, posting in [info]_scientists_
Jul. 14th, 2008 @ 02:05 pm Article request
Does anyone have access to this article and would be able to send me a copy?

J Autism Dev Disord. 2006 Nov;36(8):973-82.
Utilization of lymphoblastoid cell lines as a system for the molecular modeling
of autism.
Baron CA, Liu SY, Hicks C, Gregg JP.

If you can find it please send it to chemrocks04@yahoo.com
Thank you <3
About this Entry
[info]chemrocks, posting in [info]_scientists_
Jul. 13th, 2008 @ 03:20 pm medicated scientists
Just a simple curiosity. How many scientists on here have been diagnosed with A.D.D (Attention Deficit Disorder) and take medication whether they are SSRI's (Dexadrine, Etc) or NRI's (Strattera, Wellbutrin, Etc) and have a successful career or position in research and development or at a lab?

If it is not you personally but know of an anecdote of someone else please share.

Cheers,
Alexzander
About this Entry
[info]catalyst37, posting in [info]_scientists_
Jul. 13th, 2008 @ 12:07 pm Article request-EMERGENCY.
I need this article as soon as anyone can get it. It's for my preliminary examination and pretty much determines if I pass or not. :(

Durham, D. G. et al. Chlorination of Pyrroles. III. Canadian Journal of Chemistry (1972), 50(19), 3223-8.

pokechokey at hotmail dot com.
About this Entry
[info]norepi, posting in [info]_scientists_
Jul. 13th, 2008 @ 05:44 pm HELP!!
Dear clever generous wonderful scientist.

Here i am at work on a sunday getting a sequencing reaction cleaned up for tomorrow when I accidentl added 70% EtOH not 100%

Here are the details
1uL Big Dye 3.1
3.5uL 5 buffer
3.2uL SP6 primer (for pGEM vector)
12.3uL DNA

Clean up
5uL 125mM EDTA
60uL 100% EtOH

At this step I added 70% not the 100%.

Leave to incubate at RT for 15 min
30min spin
wash with 70% EtOH
dry pellet

Is this going to eff up my sequencing tomorrow?
Please tell me some good news?

Sincerely
Zena
About this Entry
[info]happyzen, posting in [info]_scientists_
Jul. 12th, 2008 @ 04:30 pm sources for protected unnatural amino acids
Does anyone here do/has done solid phase peptide synthesis?

If so, which suppliers did you order protected amino acids from? And do they sell unnatural or modified amino acids? Specifically I want to make peptides with phospho-Ser/Thr, methionine sulfoxide, and 3-nitrotyrosine. Sure, I can do wet chemistry on the peptides after they're synthesized, but it would be nice to have modified amino acids to start with so I don't have to worry about side reactions.

I imagine phosphoserine/phosphothreonine would be available, but I've never heard of anyone making peptides with oxidized methionine or nitrated tyrosine.
About this Entry
[info]sick_squidward, posting in [info]_scientists_
Jul. 12th, 2008 @ 04:11 pm designing oligos
this is an absolutely idiotic question that i am asking because i am paranoid,but i'll ask it anyway.

when making oligos for sequencing, is it really as simple as picking a starting region for what you want to sequence and having the computer generate oligos that are available (and picking the best one from those)? I am using the invitrogen gateway vector cloning kit and vector NTI to design primers for the BP clonase plasmids I designed; we want to make sure that the constructs we cloned into the plasmids have little sequence error. I am a summer intern and this is my first time in a molecular biology lab and my advisor's explanation for designing oligos was simple...perhaps too simple for me, hahaha.

thanks!
About this Entry
[info]cosmictofu, posting in [info]_scientists_
Jul. 13th, 2008 @ 06:56 am Follow-up question regarding Cystine Tellurite Blood Agar
Hello! Thanks for those who helped me the other day. Most special thanks for [info]lincolnparadox who suggested a reference and [info]msdna for encouraging me.

I had encountered a statement though...

Potassium tellurite inhibits the growth of gram negative organism.

How?
About this Entry
[info]plainbrownbox, posting in [info]_scientists_
Jul. 12th, 2008 @ 12:38 pm (no subject)
So I'm trying to figure out what kind of chemistry I'm interested in so that I can choose a good grad school for it, so I don't end up going to an organic chemistry school when I want to study analytical chemistry or something. Right now, I'm thinking that some sort of inorganic chemistry might be it. But my current research mentor seems to want to steer me away from that.small, rather rambling, story under here... )

I guess I'm asking for help in terms of suggestions of what I might be interested in, seeing as how I feel like my mentor is a little biased. I'm also asking what research in analytical and physical chemistry might look like. I know that I don't want to be a biochemist because running gels makes me want to cry, but yet I find the how the structure of the protein plays a role in substrate binding fascinating, so that's a little confusing, too. The kinetics of inhibition was cool, too, so maybe I'm a physical chemist...? I'm reading about the research of various faculty at various schools, and I am finding myself drawn to a fair number of inorganic chemists, but I don't know if that's just because it's something I understand, or because that was the most recent class I took other than biochem, or because of wishful thinking. :p

Help? Suggestions? Ideas? Comments? Thoughts?

Thanks for reading...
About this Entry
[info]raspberrydagger, posting in [info]_scientists_
Jul. 11th, 2008 @ 05:20 pm Another request..
You'd think a major marine biology facility would have this.. but nooo.. :(
I owe you guys big..

Lien, T. W., H. C. Hsiung, et al. (2002). "Genomic Similarity of Taura Syndrome Virus (TSV) between Taiwan and Western Hemisphere isolates." Fish Pathology 37(2): 71-75.

ISSN 0388-788X

janarock at gmail dot com

Thanks in advance if anyone has it.
About this Entry
[info]msdna, posting in [info]_scientists_
Jul. 11th, 2008 @ 11:09 am (no subject)
Is a dip in productivity normal after submitting a paper (or two)?
About this Entry
[info]harleybitch, posting in [info]_scientists_
Jul. 10th, 2008 @ 12:26 pm Science Idol: Time to vote
Current Mood: amused
Union of Concerned Scientist is hosting the voting for their Science Idol Cartoon contest, which propose is to draw humorous attention to the serious issue of political interference in science,.
To Vote click here
Theres two were my favorite:

This is the one I voted for
About this Entry
[info]anjel_kitty, posting in [info]_scientists_
Jul. 10th, 2008 @ 01:13 pm IF
Dear immunofluorescence experts:),

Have you ever stored fixed (PFA) cells in tissue culture medium overnight before proceeding to permeabilization and staining? Does this affect quality of the staining?
About this Entry
[info]sputnik5, posting in [info]_scientists_
Jul. 10th, 2008 @ 11:48 am shape-memory polymers
I remember learning about SMPs in the introductory polymer class I took for kicks back my freshman year of college.  I've been doing some [internet] research on their current availability and sort of brushing up on terms like glass transition temperature and cross-linking.  I'm surprised at how much more interesting I find this stuff (the manipulative ability) now then I did back when I was a freshman. 



About this Entry
[info]undecidedmirror, posting in [info]_scientists_
Jul. 10th, 2008 @ 11:49 am Ultrasonic Cleaners!
Hello, Scientists. I'm  a recent proud parent of a brand new Ultrasonic Cleaner (or "sonic bath") from Fisher - an FS-60. As with most things on Fisher's oh-so-user-friendly website, I didn't know I needed a perforated pan or beaker cover to submerge the items in said cleaner. I bought one, read through the manual, and gave it a test run today, but was shocked at the terrible, high-pitched whine coming from the machine.

Basically, my goal is to place either a 250ml or a tall 600ml beaker in the perforated pan with a sieve on top (the sieve openings range from 80-250 microns in size). I am essentially trying to separate 12,000+ year old pollen from clay-rich lake sediments for radiocarbon dating, and am making up a protocol as I go along (loosely based on protocols from other labs). The vibrations from the sonic bath are necessary to move the particles through the sieve (otherwise, surface tension would keep them on top and it would take hours).

Here's where I'd like some input: The perforated pan doesn't fit the rim of the bath perfectly, even though it was ordered from Fisher's website for the size cleaner I have. Could this be the source of the noise? I know that, given that it's a "sonic" cleaner, I should hear something, but this is really obnoxious. Do people typically wear ear protection when they work with these things? Can I pad the edges of the perforated pan where it rests on the basin to eliminate the steel-on-steel sound?

Oh - a year ago I mentioned that I was looking for good, comfy shoes to wear in the lab. I found the Croc Specialist, with a closed toe and heel and no holes, and I absolutely LOVE them. They're incredibly comfy, easy to wash, easy to remove, and hold up quite nicely to various drips. :)
About this Entry
[info]antarcticlust, posting in [info]_scientists_
Jul. 9th, 2008 @ 05:23 pm It's called ePmotion
Current Mood: amused
Wow eppendorf's commercial for its automated pippeting system is pretty great. I didn't know they had their own boy band on call in lab coats:
http://www.eppendorf.com/int/hawkpopup.php?contentid=13
About this Entry
[info]anjel_kitty, posting in [info]_scientists_
Jul. 9th, 2008 @ 06:04 pm (no subject)
Has anyone ever made collagen gels (or something similar), and if so, do you have any tips?

My collagen refuses to polymerize. I've done everything. I've incubated in 37°C with and without 5% CO2, room temp, etc. I've put it on slides, cover slips, treated plates, untreated plates, deep 24-well plates, thinner p100s. I've tried switching media. I've tried using NaOH vs. sodium bicarbonate to adjust the pH. I've tried switching the collagen from type I to II or III, and I've tried it with old collagen, new collagen, red collagen, blue collagen. I've tested the pH at every single step of the process. And it's not like it's a hard process, either - thaw collagen, add media, adjust pH with NaOH to taste, watch collagen gel, rejoice.

The closest I ever got was when I accidentally left a slide uncovered, and it dried out. The collagen either precipitates into a goopy mess, or it begins forming a matrix but never actually solidifies to a gel. And perhaps this is where I'm going wrong - is it even possible to get collagen to gel to a point where you can cut it into bits? I'm talking maybe jello consistency. (Preferably lime jello, but I'm willing to accept raspberry, as well.)

If this doesn't work I'm going to have to start sacrificing chickens and/or virgins.
About this Entry
[info]numinicious, posting in [info]_scientists_
Jul. 9th, 2008 @ 01:51 pm Articles help :)
Looking for a two articles:
Synthetic Metals Volume 13, Issues 1-3, January 1986, Pages 193-205 (doi:10.1016/0379-6779(86)90070-6) - this;
Synthetic Metals Volume 18, Issues 1-3, February 1987, Pages 285-290 (doi:10.1016/0379-6779(87)90893-9 ) - and this.
If anyone have access to this paper, please e-mail to serendeep (at) rambler (dot) ru
Thanks in advance

The question is solved, thanks
About this Entry
[info]niktos12, posting in [info]_scientists_
Jul. 8th, 2008 @ 03:32 pm scene from a university library
Current Mood: amused
Hope you are all as amused by this as I was.

I was in the reading room this afternoon and witnessed the following:

A girl walked up holding a shiny copy of Neuron.
She lay down on one of the comfy leather couches with her journal, turned to face the back, and fell asleep.
Twenty minutes later she woke up, walked back to the shelf and put it away.

Research by osmosis?
About this Entry
[info]vsherbie, posting in [info]_scientists_
Jul. 8th, 2008 @ 01:36 pm Another shameless request
Nucleotide sequence of 3'-end of the genome of Taura syndrome virus of shrimp suggests that it is related to insect picornaviruses.

Arch Virol. 2001 ;146 (5):941-52

I'd be forever in your debt.

janarock at gmail dot com

--

Gotta love limited uni access.. grr.
About this Entry
[info]msdna, posting in [info]_scientists_
Jul. 8th, 2008 @ 09:28 am HELP! Cystine Tellurite blood agar (Culture Media)
I'm studying Introduction to Microbiology right now and we are in the topic of culture medias. Our professor gave me a research assignment regarding to the cystine tellurite blood agar.

But I wanted to brawl my eyes out and cry! I cannot find any information about this specific culture media other than its purpose.

Purpose: Isolation of Corynebacterium diphtheriae

I tried finding information in the internet. I looked for the Journals of Microbiology in my school library but they're only a few and none of the information I need is there. I scanned the books of Microbiology but we have only 20+ books regarding the subject of General Microbiology.

I live in a 3rd world country and in not-so top school in our country that's why reference materials are very limited. So, I hope you understand.

Questions:
1. Look for the purpose. (I already have that one).
2. Identify the mechanism how the different component is useful for the isolation of a specific bateria.
3. Mechanism action
- How this particular organism inhibit the growth, what are the steps by steps of the mechanism action, what happened from the beginning to the end and why.
4. Cite the literature.

HELP!
About this Entry
[info]plainbrownbox, posting in [info]_scientists_
Jul. 6th, 2008 @ 10:55 pm Cis ring junction steroids
Does anyone happen to work on steroid/ols?

I ask because a compound I'm currently working with vaguely resembles a steroid (several fused hydrocarbon rings). One of the characteristics we believe make it a substrate for the protein we're looking at is the presence of a cis ring junction that forces the molecule into a "bent" conformation. A structurally similar molecule that lacks this bend fails to bind.

Steroids generally have all-trans ring junctures that make them globally relatively flat.

My question to the group: Does anyone know of any naturally occuring steroid/ols either from plants or animals that contain cis ring junctions? If I could find a "bent" steroid, this would completely take my project in a different, yet very cool, direction.
About this Entry
[info]immorethanme, posting in [info]_scientists_
Jul. 6th, 2008 @ 06:56 pm Lab confidence
Whenever I do an experiment, regardless of what it is, I'm constantly doubting myself. I can't help but think there's something I'm forgetting, some step I'm accidentally leaving out, or a better way to do what I'm doing.

Does anyone else have this same problem or do all of you jump head first into your project without any second-guessing?
About this Entry
[info]immorethanme, posting in [info]_scientists_