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Pawel Szczesny › Comments
what would be a bioinformatics killer app for the IPhone?
Piotr Byzia, Deepak Singh, Nakao M. and 6 other people liked this
any comments?
- Paulo Nuin
I thought about doing a colony counter for the G1 ... point it a plate , click and get a the number of colonies. This could be handy :)
- Pedro Beltrao
Mobile versions of commonly-used websites: NCBI databases, BLAST, PDB etc?
- Neil Saunders
Like Pedro's idea too. A common complaint about electronic lab notebooks is that people in the lab do not record data at a computer - so why not transmit to the ELN via phone? Better still, have the instruments tweet to the ELN :-)
- Neil Saunders
a ncbi, pubmed search?
- Paulo Nuin
Pedro's idea++. However, I don't really see a reasonable workflow with mobile versions of NCBI or BLAST on the iPhone.
- Daniel Jurczak
Neil, Paulo, Daniel, have you seen this: http://www.ncbi.nlm.nih.gov/pubmed... ? It's from 2001 :)
- Pawel Szczesny
Would there have to be one? (Or am I just narrow-minded here? Hope not...) The colony counter makes sense, but there's no real added value in blast or ncbi on a mobile phone, is there? It'd really have to be an app that leverages the fact that it can be carried around. So maybe as an input portal for your labjournal (notes, photos).
- Jan Aerts
I don't know about bioinformatics, but biology could sure benefit from a killer lab timer. :-)
- Danielle Fong
Would any aspect of bioinformatics benefit from being made mobile at all? Maybe a service that could check in on the progress of molecular dynamics calculations or something?
- Mr. Gunn
Yes, it has to be said that most bioinformaticians are rarely away from a computer long enough to require mobile access :-)
- Neil Saunders
@Pawel nice link. I will check it out.
- Paulo Nuin
@Neil: may I guess where you have lunch?
- Paulo Nuin
the monitoring visualization bits are relatively east ESP with a full featured browser. I love the colony idea. In a lab finding a sample by taking a picture of the bar code (for the g1) or using the phone as some sort of controller
- Deepak Singh
@Paulo What? You don't eat your lunch at the computer?
- Marcos de Carvalho
NCBI has persistently improved their web resources, especially in terms of UI. Whoever is behind this, you're doing a good job! Thank you!
Mr. Gunn, Christopher Fields, imabonehead and 3 other people liked this
On Wednesday mornings (GMT+2) we have a bioinformatics lab with ca. 40 students. From our experience, NCBI team chose exactly these moments for introduction of the improvements, because every second week the whole site is broken for half an hour :).
- Pawel Szczesny
Gene and protein annotation: it’s worse than you thought #bioinformatics - http://bytesizebio.net/index...
Andrew Perry, Nakao M., Shirley Wu and 19 other people liked this
I was thinking "nah, it's probably about as bad as I thought" - but you're right!
- Neil Saunders
Error level (near 0%) for SwissProt looks interesting. People of protein-protein interaction data claim 2-9% error rate on manually curated sets, and the same level I would expect from SP. Some things are better than I thought ;).
- Pawel Szczesny
Not too bad, but I think its even worse than they do. And evidence codes won't fix this. Manual curation and standards for automatic annotation are in dire need of a revolution, and even if we get that it'll still take years to fix.
- Paul J. Davis
@Paul How would you revolutionise it if all the data is still contained in the relatively unnaccessible journal article?
- Frank
Trust Pawel to see the half full (or 60% full) part of the glass. I agree with Frank though: it is not feasible to go through NR and fix the annotations manually. We just have to accept that NR, TrEMBL and KEGG are (mostly) over-annotating, and remember that when we rely on them when delving into the protein family level.
- Iddo Friedberg
Thanks Iddo. I lost count of how many times annotation errors came up in my discussion with experimentalists who lack experience with such databases. (Not surprisingly, they usually think these errors are negligible, especially when it comes to THEIR proteins.) Now I'll just send them a link to your post...
- Mickey Kosloff
NCBI RSS feeds now gives me a link to "79 new articles" instead of one article per RSS item... :-(
Egon Willighagen liked this
When number of new articles per check exceeds certain amount, NCBI provides only links.
- Pawel Szczesny
yep , it happens to me as well. I assume that Pawel is right that there is some number above which it reports a link instead of individual items
- Pedro Beltrao
It's from here: http://www.ncbi.nlm.nih.gov/bookshe... "If the number of citations retrieved is greater than the number of items displayed the feed will include a link to display the complete PubMed retrieval."
- Pawel Szczesny
Nice polymorphic API! They could also stick with one API and output more RSS entries in that case.
- Egon Willighagen
ah, ok. Thanks Pawel.
- Pierre Lindenbaum
Starting a new post doc at NKU - http://www.michaelbarton.me.uk/2009...
Piotr Byzia, Bill Hooker, Cameron Neylon and 5 other people liked this
good luck, and enjoy it
- Frank
Very cool. Wish I'd stayed with the microbial genomics. Happy to discuss it anytime!
- Neil Saunders
All the best at new place.
- Pawel Szczesny
Good luck!
- Martin Fenner
congratulations Michael!
- Jean-Claude Bradley
Thanks for the nice comments everyone.
- Michael Barton
Possibly lame question. Is there any way to write ASN.1 format under BioPerl (Bio::SeqIO::entrezgene is a parser only)? Alternatively, is there a tool that converts from GenBank format to ASN.1?
Mike Chelen and Pierre Lindenbaum liked this
I think there's a tool in the NCBI toolkit to convert between ASN.1 and other formats. Mentioned in this mailing list thread - http://bioperl.org/piperma....
- Neil Saunders
There is a binary and a text format for ASN.1. Writing the text format is straightforward. The ncbi toolkit contains an ASN1 compiler 'asntool' that reads an ASN1 format and produces the C code for reading the binary format. I tried to use it: cf. this old post: http://tinyurl.com/ybyq9x2 . Can you call those C functions from perl ?
- Pierre Lindenbaum
Neil, AFAIK NCBI's toolkit converts _from_ ASN.1 to other formats - it doesn't write it though. Similarly, EBI's toolkit doesn't support writing ASN.1. Thanks Pierre for the pointer, but since I need to write the text format only, probably it will take less time to put something together in Perl than in C. :)
- Pawel Szczesny
Ah right. Seems strange that everything is "read-only". Then again, ASN.1 is an ancient, internal format used and understood only by NCBI. They probably figured no-one in their right mind would want to write it :-)
- Neil Saunders
Unfortunately ASN.1 was abandoned in favor of XML (because it was missing some tools for non-C programs ? no tools for transformating too (xslt...) ) but IMHO, it is/was a very good way to structure the data: there is a schema to validate the data, the binary format is compact and the text format looks like and enhanced JSON...
- Pierre Lindenbaum
Pawel - the BioPerl module is based on a non-bioperl read parser Bio::ASN1::EntrezGene; have a look in CPAN. This doesn't go in the right direction for you either, but may be helpful. If ASN1 exists, something must write it! I'd ask the NCBI guys directly.
- Mark A Jensen
Also, try posting to the list : bioperl-l@lists.open-bio.org, someone may very well have done this before.
- Mark A Jensen
What would research funding look like if it were invented today? Let's start collecting materials. (via http://friendfeed.com/danielm... ).
joergkurtwegner, suze, Meryn Stol and 7 other people liked this
The basic structure for this part iii of the "what would X look like if invented today" series is in the mind map at http://www.mindmeister.com/3016825... , with background via http://friendfeed.com/search... . Main points: More flexibility in the models of funding, more attention to technological shifts in the way people (including scientists) communicate. Such has also been argued at http://ff.im/9GGRn and http://2020science.org/2009... .
- Daniel Mietchen
Just noticed that we used different notions of "public funding environments" in the mind map so far. What I had in mind was to have "funding environments" in public, much like what fundscience.org plan to do. Some of the added comments seem to have used the term in the sense of environments for "public funding". Both notions are certainly valid, and we should think of ways to keep them apart.
- Daniel Mietchen
good point re making this difference clear(er) in the map
- Claudia Koltzenburg
I would like to see a lot more funding of contests
- Jean-Claude Bradley
Yes, Jean-Claude, contests and prizes with a competitive element are definitely on the list. If you have good examples from the recent past, please post them here.
- Daniel Mietchen
"More money for science is always good. Or is it? Six experts tell Nature what concerns them most about the US stimulus spending and suggest ways to ensure that it benefits research and society in the long term." - http://www.nature.com/nature...
- Daniel Mietchen
Daniel -for a recent example of a contest for research: http://onschallenge.wikispaces.com/
- Jean-Claude Bradley
Thanks, Jean-Claude. It is noted along with http://www.claymath.org/millenn... and http://www.xprize.org/ as an effort to make the chain from achievement to award both shorter and more transparent than currently usual.
- Daniel Mietchen
Daniel - the thing I like about contests is that barrier to participation is orders of magnitude lower than traditional funding - there is no need to convince anyone that what you are attempting will actually work before doing anything. Of course this limits the type of projects that can be run but it still applies to a large number.
- Jean-Claude Bradley
Has there been any recent follow-up study to "Activities, costs and funding flows in the scholarly communications system" at http://www.rin.ac.uk/our-wor... ?
- Daniel Mietchen
The Wellcome Trust weighs in on reforming science funding: http://www.timeshighereducation.co.uk/story... - see also http://ff.im/bljS1 .
- Daniel Mietchen
thanks for the pointer, Daniel
- Claudia Koltzenburg
Let's not forget that http://www.submeta.org/ provided funding for http://onschallenge.wikispaces.com/ - certainly a "basic research" funding model that looks promising
- Daniel Mietchen
One more: http://ff.im/cHoa5 on HHMI's focus on "people, not projects" - http://pazoulay.scripts.mit.edu/docs... .
- Daniel Mietchen
Daniel, not that I have anything against HHMI, but that mantra is not exclusive to them. For example Max-Planck Society has exactly the same approach (and I would say that at 10% of HHMI's budget and having twice as much Nobel prize winners, MPG looks a bit more effective ;) ).
- Pawel Szczesny
Didn't mean this to be exclusive, and I am well aware of MPG approaches (been there for a while).
- Daniel Mietchen
"I wish there was a universal format for submitting grant proposals; authors could post proposals (once!) & then the funders bid on them." (rephrased from http://ff.im/5VwEI ). I would add that the process should be public. fundscience.org plan to go this way.
- Daniel Mietchen
How do funders and scientists rank "more attention to technological shifts" against the "scientific expertise they have"? One says "change" the other "keep doing what you know"! Are those two things not disagreeing each other? In other words, who would you fund first, the "crazy new idea" or the "conservative stuff"?
- joergkurtwegner
I would think funders should have (as they do now) the liberty of choosing their priorities, and in many cases this will be a mixture of many incremental projects and some revolutionary ones. The main shift in the system would thus be to have just ONE avenue for proposals, and to make it public.
- Daniel Mietchen
On the role of rules in creativity and innovation: http://ff.im/cRs7K .
- Daniel Mietchen
got the advice from my wife that before sleep I should relax w/ other types of literature than programming/biology & w/o backlighted screens
Itachi, Khader Shameer, Piaw Na and 5 other people liked this
Reading anything right before going to bed is bad. Give yourself at least 30 minutes to unwind: lie on the sofa, watch mindless TV - anything that requires no brain!
- Neil Saunders
I read Newspaper before sleeping and sometimes those editorials are good for sleep. :)
- ashish
sudoku...
- Andrew Su
thx guys, were staying up late in the last couple of days due to thinking on coding problems hard instead of sleeping and realized that the iPhones next to my bed are not helping me, probably will move them to another room.
- Attila Csordas
Watching TV is a bad way to go to sleep. Reading books is great.
- Piaw Na
My 'going to sleep' material is usually science fiction or fantasy.
- Michael R. Bernstein
For unwinding I find that if you include a glass or two of red wine, - all of the above works :-)
- Nils Reinton
s/red wine/vodka
- Bill Hooker
Reading books: history of Science, SF, art, comics
- Pierre Lindenbaum
Psychology books or... FriendFeed ;)
- Pawel Szczesny
a good novel is my favorite way to relax before sleep
- Mike Chelen
another problem: I'm getting a Kindle tomorrow, can I use it in the bed to read fiction, comics, art... all the light things that makes us easy more or less?
- Attila Csordas
Not comics. Fiction, absolutely
- Deepak Singh
No art or comics, just fiction and non fiction.
- Piaw Na
Can you read the H+ magazine on your kindle ? Is it color ? Let me know if you can because I need to find a good way to read this and other pdfs.
- Nils Reinton
I could give you a list of selected publications that make me fall asleep whenever I try to read them ;-)
- Lars Juhl Jensen
LOL @Lars!
- Bill Hooker
Proposal for Science 2.0 lectures - http://freelancingscience.com/2009...
Piotr Byzia, Berci Mesko, MD, Steve Koch and 7 other people liked this
I think the compatibility of IP and ONS is a very interesting topic - Steve Koch has an agreement with his research office that might make it partially compatible
- Jean-Claude Bradley
Jean-Claude, thanks for the pointer. I need to look into that. Also, Paulo Nuin commented on the blog that I could (and I will) mention data attribution.
- Pawel Szczesny
That's a great list. And data attribution and citation, maybe data management in general would be good additions. Paulo on the ball as always...
- Cameron Neylon
Agree with Jean-Claude that IP / ONS is interesting. Happy to provide any info on our very narrow and limited experience with the issue here at U. New Mexico.
- Steve Koch
Steve - hopefully we'll discuss that a bit at the ONS session in NC
- Jean-Claude Bradley
Finished a proposal for three lectures on practical aspects Science 2.0 targeted towards PhD students.
Steve Koch, Jean-Claude Bradley and arek liked this
The overview of the proposal is already on my blog: http://freelancingscience.com/2009...
- Pawel Szczesny
Complex systems and biology – introduction - http://freelancingscience.com/2009...
Piotr Byzia and Deepak Singh liked this
There're so many nice people out there - 16 hours after this posting (I finished the post on Friday evening) I got email with two useful publications in pdf format, because someone (thanks Piotr!) thought they would be relevant to the topics I'm studying.
- Pawel Szczesny
I'm glad I could help!
- Piotr Byzia
from FreshFeed
Also, that's an advantage of sharing your thoughts on a blog :)
- Piotr Byzia
from FreshFeed
More on CAS at Santa Fe Institute: http://www.santafe.edu
- Salvatore Loguercio
Thanks Salvatore. If anybody's interested many publications from SFI are available as PDFs from their website: http://www.santafe.edu/researc... I like also Francis Heylinghen's work: http://pespmc1.vub.ac.be/Papers...
- Pawel Szczesny
Hadoop World video is out - http://mndoci.com/2009...
Neil Saunders, Jeremy Leipzig, Benjamin Tseng and 3 other people liked this
Only took, what, 2 months to post this...
- Shiran Pasternak
Watching now. BTW, you've convinced me to try "hundreds of slides" approach some day - I wasn't sure it works in more scientific talks.
- Pawel Szczesny
Pawel, I wasn't sure either, but I've had a chance to do deeper dives now (at Supercomputing) and it seems to work, especially as I get more comfortable talking science in this format. If I had to choose an alternate one it would be a pure storytelling/figure format, i.e. about some of your core results and work backwards if required.
- Deepak Singh
that was a really great talk!
- Jeremy Leipzig
Jeremy, thanks
- Deepak Singh
PubMed: Next-generation gap. - http://seqanswers.com/forums...
Deepak Singh liked this
Heard at NGS Workshop that storage requirements for NGS are around 100-500 bytes per raw sequenced nucleotide and computing requirements scale accordingly.
- Pawel Szczesny
traktor tom wielki bal - http://www.youtube.com/watch...
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Saw this link on Twitter - I was absolutely sure your account has been hacked because the title is in Polish :D.
- Pawel Szczesny
No hacking here - we do this regularly.
- Daniel Mietchen
I noticed the first spam on #friendfeed :( is this the end of groups as we know it?
That's not the first, and not the last time. Fortunately, such behaviour is quickly noticed and removed. See http://friendfeed.com/friendf...
- Pawel Szczesny
Yeh, just spread around the admin status amongst trusted people within groups and then delete/report when you see it.
- Cameron Neylon
The spammers don't think much of friendfeed, and less as time goes by. They mostly focus on facebook, but perhaps friendfeed might be seen as a facebook backdoor at some point.
- Mr. Gunn
Open Science/Access challenge - http://blindscientist.genedrift.org/2009...
Claudia Koltzenburg, Jean-Claude Bradley, Cameron Neylon and 2 other people liked this
Ok if I comment here ? http://friendfeed.com/sciphu...
- Nils Reinton
Yep, sure. Comments here are also valid.
- Paulo Nuin
Is there a price for participating in this challenge ?
- Nils Reinton
The price is a poem ? ;-) http://blindscientist.genedrift.org/2008...
- Pierre Lindenbaum
no price, no reward. Wait, a reward will be a post about Open Science/Access.
- Paulo Nuin
Here's my list: http://friendfeed.com/billhoo...
- Bill Hooker
I think, to be an OA challenge, you should not have phrased it as "list of publications on PubMed or" but "list of publications freely accessible via PubMedCentral or". Anyway, mine are not all biomedical, so I go for the "or" option: http://dbm.neuro.uni-jena.de/people... .
- Daniel Mietchen
NB deleted a comment because I don't know what Paulo is up to here, but I don't want to spoil it inadvertently.
- Bill Hooker
My only OA cred here is paying the OA fee for my dissertation, and pushing for that on an upcoming publication. Also doing a lot of repository work behind the scenes.
- Mr. Gunn
Mine are here: http://www.ncbi.nlm.nih.gov/sites... 5 of 6 are OA, but to be honest I wasn't in a position to decide about a journal (or OA option) for most of them.
- Pawel Szczesny
So that Paulo doesn't have to post a link to THAT site on his blog, self-archived copies of the PDFs are here: http://www.mendeley.com/profile...
- Mr. Gunn
I'm afraid to get a virus on this link you just posted.
- Paulo Nuin
Ok I'll bite. Still working to get mine up on a single website but put a list in reverse chronological order on Paulo's blog. Basically of 12 papers since 2008, five are in OA journals, one is a CC-BY chapter in a book, and two others can be put online in final form six months after publication (which I haven't done in one case where I could). The ones that aren't proper OA I wasn't...
more...
- Cameron Neylon
"if Nature asks you for a piece you don't readily turn them down" - hard to disagree. At the same time, it's probably the best summary of the issues we are facing. Most of the discussion I had about future of science and impact of "2.0" meme onto academia were finished with a sentence along these lines :/
- Pawel Szczesny
Well there's two sides to it - one is the "Nature paper gives you credibility in grant proposals" element, the other is that it remains a more effective way of getting the message out than writing online or in OA journals.
- Cameron Neylon
Nature has been pretty accommodating - they agreed to make my book review OA http://www.nature.com/nature... - the other great thing about Nature is that they will publish work appearing on their open Nature Precedings
- Jean-Claude Bradley
That's true - I probably should have asked about that - didn't occur to me at the time...
- Cameron Neylon
Malcolm Gladwell says that if you want to shine, put in 10,000 hours - Times Online - http://entertainment.timesonline.co.uk/tol...
rich phelps liked this
I would like to see a more scientifically-based source for this meme, but like the idea.
- Kevin Gamble
It's based on work of Ericcson - here's pdf: http://projects.ict.usc.edu/itw... What everybody seems to miss about magic 10k hours is that "deliberate" practice part ;)
- Pawel Szczesny
There is prob nothing magic about 10k either... it's just the time that puts you into such a specialization, you shine because the competition does not. Something along the lines... in the land of the blind, one eye is king... or am I missing something important in the theory? Can the 10k be rewritten as function of gravity or so? Or perhaps the number of Higgs bosons per square second?
- Egon Willighagen
Pawel-- thank you for the link to the paper. Exactly the stuff that I was looking for.
- Kevin Gamble
Egon--point well taken. An issue with most things that are more complex like humans and all social science type research.
- Kevin Gamble
Looking for "What is a gene? An updated operational definition." by Pesole G. http://www.ncbi.nlm.nih.gov/pubmed... . Please email to http://is.gd/mailto:...
sent
- Michael Kuhn
Got it. Thanks a lot!
- Pawel Szczesny
#bioinformatics: you won't find on google if your cool server name was ever used before. See http://www.ncbi.nlm.nih.gov/pubmed... and http://www.ncbi.nlm.nih.gov/pubmed...
People don't realize that the server name is either unique or useless. Instead of giving you another example, here's a challenge: find a site related to bioinformatics named "project hope".
- Pawel Szczesny
GEOmetadb may be my saviour - http://gbnci.abcc.ncifcrf.gov/geo...
What about Array Express? http://www.ebi.ac.uk/microar...
- Pawel Szczesny
yes, that too, although they don't import everything from geo
- Neil Saunders
My student Brian is trying to generate a 3D model of this protein - can anyone help? AEKYKAKKAKEKAYKKKAKEAKKAKYKAKEAKAYKAEKKAKYAKAKEKAYAKAKEAKAYAKAKAKAEKAKAKAKYAEKAKAAKYAEKAAKYAEAKAKAAEAKYAAEAKEAAKAAEAKYAAKAEAAKYAAEKAAEKYAKAEAAAEAKEAA.
Nir London, Piotr Byzia, Wladimir Labeikovsky and 8 other people liked this
You might want to use Robetta http://robetta.bakerlab.org/ ... I can't since I don't have a dotedu address
- Deepak Singh
Is that a real protein? Or the Hawaiian word for "serendipity"?
- Bill Hooker
I am not sure if this helps- http://swissmodel.expasy.org/
- ashish
Bill, that's an old Iroquois war cry, if I'm not mistaken.
- Mr. Gunn
Actually it's anti-aircraft fire
- Deepak Singh
http://en.bio-soft.net/3d.html got a nice collection of diverse apps for the task, forgot to mention it when I read the post earlier.
- ElijahBailey-Zu of FF <0,
SwissModel will give you a good "first pass", if there is a target with sufficient similarity. After that, he should learn Modeller - http://salilab.org/modeller/. Though now I look more closely - that's an odd sequence, unlikely to work using homology modelling.
- Neil Saunders
This looks like a coiled-coil protein and even more, something integral to a membrane (but I'm biased towards bacterial proteins, if this one is from Eukaryote, don't pay attention to my comment). If I'm right, judging from the length it should form four-helix bundle in the membrane. As, Neil, I don't think it can be modelled by homology at all.
- Pawel Szczesny
I too was going to suggest robetta - we've had good results but the queues are pretty long ...
- Anna Croft
Thanks everyone! Brian is giving Robetta a try
- Jean-Claude Bradley
Science 2.0 in Poland – getting popular, recognized as important - http://freelancingscience.com/2009...
Piotr Byzia, Bill Hooker, Jean-Claude Bradley and 4 other people liked this
Some similar responses in Portugal from people at the OA meeting. Big opportunities for countries outside of the big four (five? six?) to steal a march by working effectively together, particularly where there is focussed infrastructure investment.
- Cameron Neylon
Cameron, it's very interesting, I would like to know more. Is there any document out there or do you know some specific names of people I could get in touch with?
- Pawel Szczesny
from email
It was all very vague - I couldn't give you actual names because it was more just a positive response to the idea in general terms, but Portugal has something called the Knowledge Society Agency or similar, so that would probably be a good place to start http://www.infosociety.gov.pt/ Will try to put you in touch with them through the conference organizers.
- Cameron Neylon
Molecular biology according to MS Word (original title: "Commentary: Never trust your word processor"). http://www3.interscience.wiley.com/journal...
Short commentary from my former colleague about MS Word correcting phrase "DNA polymerase" into "DANN polymerase" (without asking) in German medical textbooks and publications from German scientists. Unfortunately, not OA.
- Pawel Szczesny
Halogen-water-hydrogen bridges in biomolecules. - http://www.ncbi.nlm.nih.gov/entrez...
Anna Croft liked this
Is this new? I had colleagues at Southampton working to exploit F based hydrogen bonding years ago.
- Cameron Neylon
Most likely not, but I bookmarked it, as I wanted to read something up to date on the topic.
- Pawel Szczesny
Ah ok - it just seemed like a recent paper claiming that it was all new. I could see that it might be the first comprehensive look at the structural effects.
- Cameron Neylon
What's the best way to embed a pdb crystal structure into a wikipedia article? Is there a gadget that allows reader to rotate & zoom? Or is static png the way to go?
Jane Breezler, Paul Bacchus, Konrad Förstner and 4 other people liked this
How about an animated gif rotating it?
- Ruchira S. Datta
I agree that's better. I didn't know how to do it easily, so just put a snapshot in. It's my new stub article on Tus: http://en.wikipedia.org/wiki...
- Steve Koch
I realized what I actually want: A widget that will display a molecular dynamics trajectory of the system, while allowing user to rotate, zoom, pull on atoms, etc. ... Comp. people get to work :)
- Steve Koch
One of the web widgets they offer at the PDB might work in the context of Wikipedia but I would guess this is one to have a wider conversation about? Andrew Su and Tony Williams would have an idea of the logistics at least.
- Cameron Neylon
The Jmol community has been trying for a long time now to get it available in Wikipedia... you could ask on jmol-users@ ...
- Egon Willighagen
For small molecules, Noel's TwirlyMol looks nice http://baoilleach.blogspot.com/2009... , as it doesn't require plugins. But it doesn't seem to scale well for proteins.
- Pawel Szczesny
Steve, try asking on http://sciencestack.com.
- Jane Breezler
There's a long and tangentially relevant discussion here http://en.wikipedia.org/wiki.... As Egon alludes to, there is an effort to get the Jmol extension installed, but I don't see much activity http://en.wikipedia.org/wiki.... Proteopedia has Jmol: http://www.proteopedia.org.
- Andrew Su
As part of the Gene Wiki effort, we uploaded ~66k thumbnail images created by the EBI to wikicommons, and categorized them by SCOP. http://commons.wikimedia.org/wiki... Of course, they are auto-generated so they probably don't illustrate what you'd want to illustrate.. (and certainly not an MD trajectory...)
- Andrew Su
Thanks! Oh, and BTW, I was kidding about the MD trajectory, including the ability for the reader to pull on atoms in a real-time MD simulation. :)
- Steve Koch
Jmol has been up for discussion for a long time. I am not aware of any movement to support it at present. You might want to put the crystal structure hosted in Jmol elsewhere and make a link to it from the Wikipedia page rather than having it in the Wikipedia article itself.
- Antony Williams
Dear scientist, if you ask me to fax signed copy of a license which has more bytes than your program, I won't use your tool at all.
Ruchira S. Datta, Pierre Lindenbaum and Lars Juhl Jensen liked this
Majority of software written few years ago isn't available for instant download. You need to print the license, sign it and fax it to the authors. License: 1,6MB pdf; software 180KB executable.
- Pawel Szczesny
I think the biggest problem is that often the scientists didn't even want to do that. In many cases it is their institutions that force them to put their software under a cumbersome license.
- Lars Juhl Jensen
I have 12 Google Wave invites - who wants one?
Hmmmm. I'm begging for one ^_^
- Cassie peakie
Oh, and you'll have to leave your email, or I can't invite you...
- Björn Brembs
cinnamonstyck@gmail.com<-----me
- Cassie peakie
I'd like one! organelas at gmail dot com
- Bruno C. Vellutini
Yes please! gray.noah at gmail dot com
- Noah Gray
edmund.dipple@btinternet.com much appreciated!
- Edmund Dipple
please send me an invite... ms.ashley88 at gmail dot com it would be greatly appreciated!
- Laura
Ok, there's one left, everyone who contacted me so far got one
- Björn Brembs
on my knees for one dahaniel at googlemai dot com :)
- Dahaniel
Done, all gone!
- Björn Brembs
was i able to get one?
- Laura
Wow, that was quick, less than 10 minutes...
- Björn Brembs
and me?
- Dahaniel
:D
- Dahaniel
Nice social experiment
- Egon Willighagen
@Laura and Dahaniel, yes you're on the list
- Björn Brembs
thank you so much!!
- Laura
I'm watching my inbox with sad, hopeful eyes....^_^
- Cassie peakie
thanks! lucky me that I stayed for the Vodka session in our lab, otherwise I would have missed it :)
- Dahaniel
I thought I'd set this off and then check in the morning. Good I waited for a few minutes...
- Björn Brembs
yes please - simoncoles@gmail.com
- Simon Coles
did you send them already? nothing in my inbox or in spam...
- Dahaniel
All the emails are now with Google. I have no idea when they'll send the accounts out. Last time around, it took a couple of weeks.
- Björn Brembs
Thanks Björn!! Just got in..
- Bruno C. Vellutini
Thanks Björn; just got mine today...
- Noah Gray
I could use one, please -- PeterAtOhioLINK@gmail.com
- Peter Murray
OK, Peter, you've been invited.
- Carl Fulp
Carl - I could use one, if you have any free - simoncoles@gmail.com
- Simon Coles
OK, Simon, you've been invited.
- Carl Fulp
Many thanks, Carl.
- Peter Murray
I have 15 or so left.
- Brian Krueger - LabSpaces
dupuisj@gmail.com if anyone has an invite left. Thanks!
- John Dupuis
If anyone has any left: bentleywg@gmail.com . Thanks!
- Betsy (bentley) Vera
I invited you John
- Christina Pikas
@christina, I did too :P Got one for you too Betsy.
- Brian Krueger - LabSpaces
For everyone here, feel free to invite me (whatever that means): gray.noah@googlewave.com
- Noah Gray
May I have one too? pawel at FreelancingScience com
- Pawel Szczesny
Yeah, feel free to add me to your contacts... brian.j.krueger@googlewave.com
- Brian Krueger - LabSpaces
Brian: Thanks! (c'mon, gmail)
- Betsy (bentley) Vera
I invited you, Pawel.
- Carl Fulp
Thanks Carl!
- Simon Coles
I lost track, if there is still some invites in the mix, but if so, feel free to invite the olchemist at gma!l dot çom
- Oliver Schuster
ppl, I have several invites, if anyone needs. Just invited you, Oliver.
- Bruno C. Vellutini
I've received my invite, but how does one get invites to give away? Did I miss a message somewhere?
- Mickey Schafer
that is also my question. I got invited quite a while ago, playing a little, but could not find a way to invite others?
- Bora Zivkovic
have yet to receive an invite :(
- Christopher Harris
I think those who received the invitation from Google itself got 20 invites to give (there is a wave with them). People invited by a regular user that had invitations can't invite others.
- Bruno C. Vellutini
Carl, invite just came. Thanks a lot!
- Pawel Szczesny
Carl, my invite just came through - thanks!
- Simon Coles
hey anyone have an invite i desperately want one Cyberfennec (att )gmail(d 0t)c0m
- keegan maloney
Does anyone know the impact factor of PLoS One?
Jean-Claude Bradley liked this
Does it have one? I thought Thomson refused to calculate IF for it.
- Pawel Szczesny
Pawel's right.
- Björn Brembs
Thank you, that's what I needed.
- Berci Mesko, MD
pertinent: http://www.sciencebase.com/science...
- Björn Brembs
The main product of academia is not knowledge but the reproduction of academia. - http://news.ycombinator.com/item...
'Mummi' Thorisson, Benjamin Tseng, Claudia Koltzenburg and 6 other people liked this
"In fact, in the life sciences, the back and forth is getting more common, and will increasingly get so as the models for research, esp in large scale biology change. On the CS side there are any number of examples as well."
- Deepak Singh
To paraphrase Ken Robinson: the purpose of academia is to produce university professors.
- Pawel Szczesny
It's kinda like law ;)
- Benjamin Tseng
Short question: is there any up-to-date (let's say 3rd quarter of 2009) estimate how many scientific blogs is out there? If you have no idea, please give your own estimate. Biased consensus is better than nothing ;).
Piotr Byzia and Khader Shameer liked this
blogs.nature.com lists ~700 blogs
- Pierre Lindenbaum
technorati http://technorati.com/search... Blogs relating to “science”: 14740 blogs
- Pierre Lindenbaum
Thanks Pierre, Research Blogging (partially overlapping) with the lists above ~950 blogs.
- Pawel Szczesny
My guess would be 1000-2000 with two thirds of those being rarely updated. Bora probably still has the most complete list.
- Cameron Neylon
My guess would be in the 1000 of them. This does not include non-scientific blogs written by scientists
- Deepak Singh
I reckon ~ 1k blogs written by science professionals about science too, with 30-40% being actively maintained...
- Euan
Not more than 200-300 active ones
- Nir London
Thank you all. It's so little? I thought it's way more than 10k by now. It seems I wasn't offline for _that_ long ;)
- Pawel Szczesny
My guess is similar to those above -- maybe 2-3K blogs total, only about 500 active. But that's "blogs written by scientists or educators or librarians or other science professionals", not "blogs that sometimes mention something science-y"; I suspect the Technorati figure is about right for the latter.
- Bill Hooker
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