 |
|
| FriendFeed is the easiest way to share online. Learn more » |
Pepe JG › Likes
"Top 20 Websites Every Scientist (or engineer) ought to know" by Mary Spiro http://www.zangani.com/node... (via http://friendfeed.com/the-lif...)
YouTube channels for life scientists? Does a listing of these exist anywhere? Or, can we start one here--list channels you know of?
Mr. Gunn, Pepe JG, Michael Nielsen and 8 other people liked this
SciVee is described as 'Youtube for scientists', isn't it? http://www.scivee.tv
- 'Mummi' Thorisson
http://www.youtube.com/user... - original video content from Nature
- Euan
Well, there is http://www.dnatube.com/ also, and thousands of scattered youtube playlists...
- Bruno C. Vellutini
I'd like to see added a listing of (audio) podcasts for life scientists.
- Jason Miller
Thanks Bora! Do you want to collate these, or should I?
- Mary Canady
I am sure there are more - anyone else has ideas? Please put them somewhere in one place then let us know so we can spread the word.
- Bora Zivkovic
One of my favourites: http://www.youtube.com/user...
- Bora Zivkovic
Cell press has a great YouTube channel. Also check uni channels
- Wladimir Labeikovsky
from BuddyFeed
A huge list of video sites for life scientists. http://scienceroll.com/2007...
- Berci Mesko, MD
Genera/Medicine/Life Sciences: http://www.youtube.com/user... ; http://www.youtube.com/user... ; http://www.youtube.com/user... ; http://www.youtube.com/user... ; and http://www.youtube.com/user...
- A Roy
It's not YouTube, but JoVE is pretty neat: Journal of Visualized Experiments: http://www.jove.com/
- rnaworld
OK, here's the compilation of video resources for scientists http://sdbn.org/sciencevideos Additions/edits welcome!
- Mary Canady
Not a YouTube channel but certainly an interesting resource for video lectures is at http://www.world-lecture-project.org/ .
- Daniel Mietchen
Cold Spring Harbor has a rich video archive of scientists talking about their research lives, etc.
- Maxine
(For a friend) What would be your preferred graph drawing / analysis package for drawing a 90K+ node graph?
Abhishek Tiwari, Pepe JG and Mike Chelen liked this
I've suggested looking into Pajek (http://pajek.imfm.si/doku.php) and Walrus (http://www.caida.org/tools...) for drawing (though these are older packages) and Boost (http://www.boost.org/doc...) for analysis. Graphviz seems to choke on more than a couple hundred nodes, although they supposedly have a new package (SFDP) for large graphs. Have I missed anything great?
- Hilary
igraph for analysis
- Rajarshi Guha
I second igraph; cross-platform, libraries for ruby/python/R, works very well - http://igraph.sourceforge.net/.
- Neil Saunders
cytoscape?
- Andrew Su
yEd has tantalizingly awesome large graph layouts. Though its both non-FOSS and Java which is two-strikes-you're-out land.
- Paul J. Davis
From Beth Weil, head librarian at UCB "Berkeley's Research Impact Initiative turns one year old today. So far we are very pleased with the results. We have received 40 requests for funding, indicating that there is interest and a need for funding of open access journal articles.
Mr. Gunn, Pepe JG, Donnie Berkholz and 2 other people liked this
There is more good news for UC journal authors. The California Digital Library (CDL) and Springer have signed a ground-breaking agreement in which UC-authored articles accepted for publication in most of the 1700 Springer journals will be published using Springer "Open Choice" which brings with it full and immediate access to all readers. This means that UC authors will pay no additional publication fees in order for their articles to be immediately and fully open to all. Under the agreement, articles will be published under a license in which authors retain the right to distribute and re-use their articles freely.
- Jason Stajich
To invoke the "Open Choice" option, UC authors will select a UC campus affiliation from a drop-down box that appears on the acceptance screen which authors must complete once an article has been accepted for publication. A message on the acceptance screen will indicate that the Open Choice option is being made available to them at no charge. (The Open Choice publication fee would...
more...
- Jason Stajich
What kind of PCR primer design methods and programs do you use?
Alexis biochemicals, Aarthy, Richard P Grant and 6 other people liked this
Applied Biosystems Primer Express, mainly because we use a lot of MGB probes.
- Nils Reinton
from twhirl
um, I look at the sequence and count 18–21 bases?
- Richard P Grant
+1 Richard :) I was of the same mind, when I did such things. My favourite student question was "how do I design primers for gene expression?" Answer: you need one at the start and one at the end.
- Neil Saunders
Yep, by hand (hell sometimes on paper!) but then I guess I'm old fashioned. I wasn't even allowed to use PCR until the second year of my PhD and then it took us 12 months to get it working (not quite old enough to have been using multiple water baths thought)
- Cameron Neylon
NCBI has a new primer tool that uses primer3 and BLAST http://tinyurl.com/5tk67z
- Steven
I like Primer3Plus at http://www.bioinformatics.nl/cgi-bin...
- Dave Bridges
I find it odd when PhD students come into the office and don't know how to design PCR primers. Don't know what they're teaching them in the lab. I used to design mine all by eye on printouts in my wet days, and it worked just fine. Just point everyone to primer3 now.
- Daniel Swan
I used Primer3 and some obscure Mac System 7 applications. Sometimes it is easy as counting the nucleotides, but if PCR was so simplistic as that science would be much easier.
- Paulo Nuin
I'm partial to WebPrimer: http://seq.yeastgenome.org/cgi-bin... - it's not just for yeast by a long shot. Rather like Cameron, I didn't get to do a PCR until I was a postdoc. :-) But Steven's link looks good; I used to check that I would amplify something on genomic DNA by using http://genome.ucsc.edu/cgi-bin...
- Heather
Paulo, it's 2008. PCR, 90% of the time *is* that simplistic. I teach the students I have lab responsibility for to do it by eye, and to BLAST what they get to check for uniqueness. I started off by doing it on the Mac, years and years ago, but haven't used a primer design program since about 1999. And Cameron, it sounds like we started doing PCR about the same time. Worked first time for me, but took about 3 weeks to make the reagents.
- Richard P Grant
Yes, Richard, has been a while that I hadn't been to a lab doing PCR, maybe since 2001 or 2002. But depending on the availability of similar sequences the only way to go is with a program that at least gives you melting temps and some other conditions.
- Paulo Nuin
That's why I like ordering from Sigma—you get a melting temp calculation when you enter the sequences. But I only ever use that to match primers, rather than trying to differentiate between different sets.
- Richard P Grant
my primer and overall DNA experience is rather restricted to human, mouse and rat mitochondrial genome and the circular mtDNA is a different, inclusive world, I did manual design and primer3 too
- Attila Csordas
I've used a couple programs, but unless you're needing primers frequently, Richard's method is probably the best. Check for uniqueness and Tm, then order the two best looking pairs.
- Mr. Gunn
'Richard's method is probably the best'—can I put that on my CV? ;)
- Richard P Grant
I typically use vi and this primer checking tool at IDT (http://www.idtdna.com/analyze...). And WebCutter or ApE just to check my restriction sites are sensible.
- Andrew Perry
@Richard: sure you can, just credit the quote to "some d00d on teh internets" and your credibility is sure to skyrocket. :-)
- Bill Hooker
*laugh*
- Richard P Grant
Stratagene's design tools + Vector NTI
- Aarthy
Forgotten experiment may explain origins of life - http://blog.wired.com/wiredsc...
Alexis biochemicals, Pepe JG, Ian Holmes and 4 other people liked this
"There's a lesson here: don't throw anything away."
- Shannon McWeeney
This is why it's better to dry SDS-PAGE gels and keep them too, rather than just scan them (something I have to admit, I don't always do). You can always cut out the bands and run mass spec years down the track ....
- Andrew Perry
Whatever happened to Pedro of Pedro's List? - http://homepages.cs.ncl.ac.uk/phillip...
Sally Church, Pepe JG, Deepak Singh and 4 other people liked this
Pullquote: "It turns out that Pedro was, in fact, Pedro Maldonado Coutinho who was a graduate student at the time. A little more poking uncovers his thesis from 1996; this explains why he stopped maintaining the list. A little more poking reveals very little [...] Pedro, early web pioneer, I salute you!"
- Bill Hooker
Yeah, a couple years ago many folks mentioned Pedro's page. I happened to find the other day and noticed that nearly all the links are now dead (no duh!). Anyhow from what I can assert, he's a Professor in the Department of Chemical and Biological Engineering at the Instituto Superior Técnico (Lisbon, Portugal)
- Ricardo Vidal
very famous and useful list at the time
- Paulo Nuin
Totally forgotten about this! I used to use it all the time. Probably one of the first biological web resources that got me into, well, biological web resources.
- Neil Saunders
Wow. That takes me back. Perhaps there should be a Pedro, recognizing innovation in web tools for biology. The prize: a bottle of port!
- Todd Harris
Blast from the past!!!
- Deepak Singh
PHD Comics: The Economic Meltdown - http://www.phdcomics.com/comics...
Pepe JG, Michael Habib, Enro and 11 other people liked this
The Economic Meltdown: Should you be concerned? Find out in this handy decision chart
- Duncan Hull
from Bookmarklet
very smiley detour in the midst of thesis writing ;) // 've got a post-doc lined up
- Yaroslav Nikolaev
Sigh. I am doomed.
- Shirley Wu
We are all doomed...
- Duncan Hull
Just some of us are more doomed than others....
- Cameron Neylon
La la la la I can't hear you la la la la
- Bill Hooker
Everyday Science: Scans From a Science Magazine, 1919-1921. - http://chris-coltrane.livejournal.com/378327...
Pepe JG, Shannon Jiménez, Kevin Z and Jo Brodie liked this
"Stand-up comedian Chris Coltrane discovered some 90-year-old science mags in his attic. Highlights include a Tube train that doesn’t need to stop, a discussion about whether the Earth is flat, and musings on whether we’ll ever harness the ‘horsepower’ of the atom. Awesome!" Comment and link found via here:- http://network.nature.com/people...
- Graham Steel
Bench Marks » Blog Archive » Zotero facing a lawsuit - http://www.cshblogs.org/cshprot...
Pepe JG, Dave Bridges and Martin Fenner liked this
Seems fairly frivolous. If converting file formats constituted infringement, Microsoft would have crushed Open Office years ago.
- Chris Miller
Very good point about open data formats. If an application goes down for whatever reason, you can then transfer your data to a different application.
- Martin Fenner
Martyn Daniels, of the UK Booksellers' Association (digital arm) adds his take here http://bookseller-association.... "Whatever the outcome it has certainly raised the awareness of many to the open source tools that are now being developed aimed at changing the old order and bringing in the next generation of research tools."
- Maxine
Clearly frivolous, as Chris says. Even the DMCA allows reverse-engineering for interoperability, and that's about as strict as it gets.
- Donnie Berkholz
Talk by Jonathan Eisen on OA - http://scienceblogs.com/pontiff...
Pepe JG, Maureen, Bill Hooker and Bora Zivkovic liked this
Other ways to read this feed:
