Useful links about basic science topics

[Fixed Gear]

So, here are two links I use frequently:

Primer3: a web interface for designing primers for an imput sequence. This link puts you at the source code page. Just click 'user interface' and you're ready to roll
http://frodo.wi.mit.edu/primer3/primer3_code.html

Ensembl: a database for genetic/genomic architecture. I use it to find promoter/enhancer sequences for designing primers and amplicons (with Primer3) for ChIP and also to find exon/intron splice sites so that my amplicons for Real-Time PCR span a splice site such that only cDNA and not genomic DNA is amplified.
http://www.ensembl.org/

WI SiRNA design program: a web interface like Primer3 for designing RNA hairpins to silence RNA expression. Run by the Whitehead Institute of MIT, a user inputs a mRNA sequence and the program gives specific short hairpins to knockdown gene expression. You need to make a username and password, but it's free and worth it.
http://jura.wi.mit.edu/pubint/http://iona.wi.mit.edu/siRNAext/home.php

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[Treg]

Sequence Manipulation Suite This is an awesome set of web-based programs for converting DNA to Protein, calculating molecular weights, getting rid of the NCBI formatting for sequences, etc.

ISI Web of Knowledge Your institution requires a subscription. Good for finding out journal rankings and where papers have been cited elsewhere

Treg

 

[EvoDevo]

Placing on a semi-permanent sticky.

 

[EvoDevo]

How to Read a Scientific Article:

http://forums.studentdoctor.net/showthread.php?t=149866
and the original source: http://www.fiu.edu/~collinsl/Article reading tips.htm

 

[leverp2000]

I have a couple more to add:

Protein Data Bank-has all of the structures that are out there:
http://www.rcsb.org/pdb/

Restriction Enzyme Cutter (great for plasmid design):
http://tools.neb.com/NEBcutter2/index.php

Peptide properties calculator (for hydropathy, percentages of amino acids, etc.) and the oligonucleotide counterpart:
http://www.basic.nwu.edu/biotools/ProteinCalc.html
http://www.basic.nwu.edu/biotools/oligocalc.html

 

[tedrik]

This is my favorite site for finding out the hottest topics in almost any scientific field.
http://www.sciencewatch.com/

This is a related site that lets you see who are publishing the most papers in recent years for your field. It is similar to the ISI cite, but it doesn't require a university subscription.
http://in-cites.com/top/2004/index.html

 

[Kajika]

NCBI has several searchable online fulltext texbooks.
NCBI Bookshelf

 

[Fixed Gear]

I think I have used the Sequence Manipulation Suite site posted by Treg about 12 times since she posted it. Thanks, T-Reg.

 

[Treg]

I think I have used the Sequence Manipulation Suite site posted by Treg about 12 times since she posted it. Thanks, T-Reg.

Hey, I am glad you like it. I think it is the only thing of its kind that puts all those simple tools into one interface, web-based at that (access from anywhere, even the library).

Treg

 

[Sonya]

funding based on professors name

http://crisp.cit.nih.gov/crisp/crisp_query.generate_screen

 

[Man In The Box]

Man, this is a great thread.

 

[BloodMountain]

Protocol Online - "Lab's little instruction book. For an exhaustive rundown on the hottest methods in molecular and cell biology, click over to Protocol Online. The site links to hundred of protocols from commercial and research labs and hosts a helpful Q&A forum." [Science Aug(13); 285(5430)].... also has a forum... useful, but

Biowww.net - resources focusing on lab bench work related troubleshooting, methods and reagents, discussions in molecular biology, cell biology, genetics, immunology, neuroscience, bioinformatics and proteomics research....and a USMLE section? (nothing compared to this SDN's, of course); cited in Science magazine's nextwave 31 Jan 2003 issue "Seven Resources for Young Scientists".

Cell and Molecular Biology Online lists online resources for cell and molecular biology research protocols. Most of the web sites focus on particular research techniques....the parent site looks helpful too.

Elsiver MDL Elsevier MDL is the pioneering leader in discovery informatics. Over 1,000 life science companies supercharge their discovery engines with MDL software solutions to generate fresh ideas and make breakthrough discoveries. By synchronizing and streamlining the sharing and management of vital information and knowledge, we enable scientists to work more efficiently....different than the other three... slick & corporate; it's not all free but you can download their "no fee software"& see what happens

 

[lumanyika]

click here and enjoy!! UW's Video Library of 100s of scientific presentations (you can search by topic)

 

[neoserenity333]

click here and enjoy!! UW's Video Library of 100s of scientific presentations (you can search by topic)

that site doesn't exist anymore (or at least it didn't work for me)

 

[MrMunkily]

Ooh - I'll add!

NIH Lecture Videocasts!
Some are NIH only, but a lot of the good stuff is open to all interested humans.

Today's stuff is here:
http://videocast.nih.gov/

And archives are here:
http://videocast.nih.gov/PastEvents.asp

 

[NUKid]

I had a paper published last year and would like to see who has cited the article in any publications. Is there some website that keeps track of this...very interested to know. It was published in the Journal of Neurochemistry.

Thanks,

NUKID

 

[cicenhour]

The National Postdoctoral Association - www.nationalpostdoc.org
Has lots of great information for those in or considering a postdoc!!

The NPA Store
Your source for Official NPA Gear!!

 

[combioguy]

Here's another site that could be really useful. The site is SIPHS - A Life Sciences Community and is like question and answer service provided by Google Answers but is completely free to use. It also has a search engine that lets your search through forum posts found on protocol-online and the biotechniques forums.

 

[mdphddermo]

These are my favorites for Molecular Biology

Pubmed

Molecular Biology Protocols Bioinformatics

Peptide

 

[neoserenity333]

http://sciencecareers.sciencemag.or...icles/2590/choosing_a_thesis_lab/(parent)/158

great article on how to pick a thesis lab, written by an MD/PhD for MD/PhDs.

 

[tbo]

I had a paper published last year and would like to see who has cited the article in any publications. Is there some website that keeps track of this...very interested to know. It was published in the Journal of Neurochemistry.

Thanks,

NUKID

Old-ass answer to an old-ass question. The link up-top to ISI Web of Knowledge/Web of Science is the answer. Also Scopus is a new citation database but it's so new that most institutions do not own a subscription.

 

[PamEganNP]

One site I admit I spend a good bit of time at is the Vitamin D3 Blog. The author keeps track of news and developments related to vitamin D, vitamin D deficiency and the preventive properties of vitamin D3. It is extremely well-sourced, and the author / site owner always provides references for any statement or claim made on the site, so readers need not ever take the author at his or her word.

 

[JetsSBXLIII]

Harvard Primer Bank - database of tons of primer sequences, most of them validated

http://pga.mgh.harvard.edu/primerbank/

The site I probably spend the most time on:

http://whatshouldwecallgradschool.tumblr.com/

Seriously, it's hilarious

 

[floren_123ce]

Really useful thread!