My Labonews

This fantastic tool saved me a couple of OD measurements yesterday night!

Link: http://rna.tbi.univie.ac.at//cgi-bin/RNAfold.cgi

If you ever wondered how a given RNA sequence will fold in 2D, look no further... The RNAfold webserver calculates graphical images in diverse formatsof the structure based on different energy criteria you can choose. Looks a bit more powerful than the mfold server I used to use for this... Isn't nature just beautiful?

Link: http://www.wikiprofessional.org

Through Boing Boing, I came across a new Wiki project, focused at creating more precise and reviewed (as opposed to automatically generated by scanning databases) resource for proteins and their signaling pathways. I think it is an interesting concept, and although I'm opposed to creating a million different Wikis, this one has a nice interface and makes adding your insights quite easy. For example, I often refrain from editing huge Wiki articles about my field of subject, so this site is rather aimed at creating connections and adding references. Of course I couldn't resist updating the information about the universe's most important protein. Motivated (bored) scientists welcome! More info (PDF)

Link: http://www.ncbi.nlm.nih.gov/projects/GeneRIF/GeneRIFhelp.html

This may be highly irrelevent to any non-scientist, but maybe one or two of you anonymous researchers could make some good use out of it. I feel that a lot of scientific and bioinformatics tools are available free on the net, but often unknown to the (young) user. I stumbled upon GeneRIF while trying to make some sense of microarray data and going through extensive gene lists. It's a service provided by the well known Pubmed / NCBI service. It basically gives you the chance to see relevant references relating to a given gene, with a one sentence summary. Everybody can contribute to it, make suggestions and corrections, and it helped me a lot making sense to the results. Although that ment going through some 100+ publications these last weeks. It allowed me to make some working model, and a lot of ideas about how to test them. Furthermore, I found the Database for Annotation, Visualization and Integrated Discovery (DAVID) that allows filter and cluster your microarray data according to gene onthology or functional relationship etc. Make good use of it, and don't forget to keep using Papers for archiving and organising your publications and bibliographies!

Link: http://www.acc.umu.se/~emilk/

Found this tool on the Badscience blog. And it sure seems to be phun!

Link: http://scienceblogs.com/evolvingthoughts/2008/02/basic_concepts_in_science_a_li.php

This is a wonderful collection of the basic principles and concepts in science. Highly interesting for ANYBODY interested in how science works. Quoting:

This is a list of the Basic Concepts posts being put up by Science Bloggers and others. It will be updated and put to the top when new entries are published. If you are not a Scienceblogger, email me and let me know of your post, or someone else's. If you want suggestions for a topic to write on, just ask. John Wilkins

Link: http://www.microsynth.ch/

I used their services now for several times for plasmid sequencing and they are really very good at it, I must say! They receive the plasmids usually the day after you've sent them in, and results are normally obtained after 1 further day. I am especially happy as they managed without major difficulties to sequence my multi-shRNA plasmid, as a single shRNA in a plasmid is usually a huge problem for the sequencers because of the stem-loop. They can do the primer design for you, you can send them your sequence or include your own, and they offer a heck of a lot of further services that did not concern my order... I can only recommend them!

Link: http://molbiol.ru/eng/scripts/01_12.html

For some time I had been looking for a simple tool to just reverse the 5' to 3' direction of DNA sequences without showing a reverse complementations, e.g. for ordering oligos. This site offers all this and more, a nice bookmark in case you don't rely on those fancy aligning applications.

I was never a big fan of those multi pipettes... The always made me feel like losing the control of what I was doing, and I suspected them of being rather imprecise. But now I had to do a titration with 8 different dilutions, 4 different cell types, 4 different conditions, 2 different compounds and the whole thing in triplicates leeding to 432 wells filled each with roughly 20'000 cells... So after considering doing this by a single pipette (you'll need a couple of hours for that), I considered using our 12-channel programmable Multi Pipette. What a relieve! You can pipet, mix and purge the tips and the programmation is very straight forward.

Link: http://www.addgene.org

A Better Way to Share Plasmids Addgene is a non-profit organization dedicated to promoting sharing of plasmid constructs described in published literature. Addgene stores original plasmid samples submitted by scientists and distributes them for use in advancing life science research. I tried their service by requesting a multiple shRNA vector and was amazed by their fantastic service, documentation (plasmid maps, protocols, references...), delivery and organization. Everything went fully automatic without any hassles, from the MTA from to the finaly delivery of the plasmid in form of an E.Coli colony in an agarose tube. Highly recommendable!

The latest public release of Papers now features finally output of your database into Endnote (buhhh) and BibTeX (yeahhh). Just thought you might like to know...

Link: http://mekentosj.com/papers/

 Another great app by the makers of EnzymeX comes now as a public preview : It's simply called papers, and it has this name not by coincidence. It's a great tool, playing in (or at least aiming for) the league of Endnote et al. Here's what the publisher writes, why not give it a try:

Papers bundles all the great technologies that come with MacOSX Tiger to give you a complete new workflow for reading scientific articles. You find, download, archive, and organize all your articles within a single application. But that is just the start, using spotlight you instantly find back the paper you are looking for. Read it fullscreen, add your notes, send a copy to a colleague... These are just a few of the many features that after using them yourself you will never want to give up again...

Link: http://www.ebi.ac.uk/2can/tutorials/index.html

Check this tutorial site out:

This site provides short and concise introductions to basic concepts in molecular and cell biology and bioinformatics. The main emphasis is placed on making it as easy as possible for the user to understand which tools and databases are available from the EBI and from sites belonging to its collaborators. The site content aims to make these services easier and more accessible but also provides links to other sites where similar resources are maintained and well supported.

Link: http://gentle.magnusmanske.de/

This Open Source tool proved to be quite helpful in calculating complementary nucleotide strands which you can easy Copy/Paste... But it is much more, quoting : GENtle is a software for DNA and amino acid editing, database management, plasmid maps, restriction and ligation, alignments, sequencer data import, calculators, gel image display, PCR, and more.