“Dear life science experts of the FriendFeed-o-sphere: Does anyone know of a good program for producing clearly annotated maps of circular genomes; ideally for mitochondia ?”
I have used A Plasmid Editor (ApE) -- http://www.biology.utah.edu/jo... which is platform independent. If you have the genome annotated in Genbank format, it will generate a graphic with the structures annotated. Here's an example of a plasmid that I made and used ApE to make a graphic out of: http://kamrani.net/kambiz/file... Let me know if you have any questions, I can provide a more detailed set of instructions (kambiz@anthropology.net) - Kambiz Kamrani
Ideally it would take a Genbank format (or similar) file with gene annotations, and produce a nice (publication quality ?) picture. Maybe one of the programs for drawing plasmid maps would be good also for this purpose ... I've never seen one I liked but I'm sure it's out there. I'm also familiar with MitoWheel (http://mitowheel.org/mitowheel...) ... it's pretty but only does the human mitochondria, and has a sequence window obscuring the diagram. We want to display various other mitochondrial genome maps. - Andrew Perry
I see, Andrew. Do give ApE a try. I just updated my previous comment with an example of a plasmid graphic I made using ApE. - Kambiz Kamrani
Being part of the Mitowheel developer team I can connect you with the real guy behind, called Gabor Zsurka. Your problem does not seem to me the toughest coding challenge comparing to what Mitowheel already knows. - Attila Csordas
Kambiz: Yes, I'll check out ApE .. my first comment wasn't actually in response to your initial one, it was just extra info .. you were too quick in responding for me ! Thanks ! - Andrew Perry
Attila: That would be great .. I have intended to email him about it anyway, since I think mitoWheel would have far greater utility if it could do any (or many) mito genomes. Unfortunately I'm actually asking for a student in the lab who needs a solution rather ..err.. quickly, so I figured Gabor wouldn't be able to meet her deadline :) In the long term, however, an updated mitoWheel would be excellent. - Andrew Perry
I actually remember trying ApE years ago now ... it's really improved, and I'll probably use it to assist my cloning in the future. Unfortunately, there are too many features (ie ORFs) on many mitochondrial genomes to display everything neatly with ApE ... I need to be able to enlarge the circle, and only display the short gene names (Genbank /gene, not /product) written around the circle, basically the way mitoWheel does it. It might fit if we hand edit the features and tweak the ApE source a little ... - Andrew Perry
"Question: Are you as obsessive as he is?
Bale: Listen I think that you know I get obsessive, but over shorter terms you know. Obviously a movie lasts a few months and then you're done with it. With him it's life long of this single obsession. This one particular trick that he knows will make him immortal. So I have an obsession, but it's a different kind of obsession. It's more kind of short term obsessions." - Attila Csordas via Bookmarklet
I do keep my text books and do read or refer to them regularly. - Kambiz Kamrani
I hadn't had money to buy many textbooks. I keep the few I have. - PauloNuin
I sold pretty much anything I could get a reasonable amount of money for. I still ended up keeping quite a few and rarely, if ever, refer to them. - Chris Miller
I kept them all, but only brought five with me when I moved: Biochemistry, Organic Chemistry, Human Physiology, Chemical Principles (Zumdahl) and Introduction to C. - Eva
Books (unlike the previously discussed papers) I love to keep around. I also make a habit of picking up old textbooks (especially genetics ones). Have a couple of great early 1900s books. It's such a great way to capture a snapshot of the state of 'condensed' knowledge at the time, the fact the information dates just part of the charm. Mind you I'm hte kind of person who would desparately like to turn one of their bedrooms into a fully fledged library ;) - Daniel Swan
I really like the PDF and Book deals that have arrived recently: book to read on the plane, PDF to search later. Perfect. - Matt Wood
Daniel, I still have most of the classic books in the field. They look good :) - Deepak
I have some, not all. Like Daniel said, I keep classics, but I sell or donate others. I go digital (much easier to find something that way) - Andreas Matern
I used to keep all of my textbooks, but as a lifelong student, that became unwieldy. Now I keep only books that might be considered seminal in the field, or ones I particularly like, or ones that are less than 5 years old...actually, come to think of it, I end up keeping most of them anyway. :-) - Timothy Driscoll via Alert Thingy
and if I want a real approximation of 'new handshakes' just for the people who are not familiar with each other, we have to take the number of all handshakes minus the number of handshakes made by people already acquainted with each other - Attila Csordas
I also get 4950. (Every person shakes the hand of 99 others, but divided by two because it's one handshake per two people.) - Eva
I like empirical tests: what if we actually measure the number of new handshakes at BBCamp? - Attila Csordas
X - 99 handshakes, Y - 98 handshakes, Z - 97 handshakes... (cut out due to Friendfeed comment limit) ... XXX - 2 handshakes, YYY - 1 handshake. 4950 together or my Perl installation is broken. - Pawel Szczesny
"A small group of researchers is meeting in Birmingham, UK, later this month to plan a free digital library of mathematics.
All the mathematical literature ever published runs to more han 50 million pages, with around 75,000 articles added each year. Over the past decade there have been several attempts to make this prodigious body of work accessible in a single digital archive, but so far none has succeeded." - Attila Csordas via Bookmarklet
1 supporting reason it is worth convincing a Nobel laureate to blog: yo has probably enough time to blog. But by blogging even the Nobel laureates will quickly lose their "exclusive celebrity status" and this is a trend I really like: being transparent on the web solves the interpretation problem of the "big man from the point-of-view of the footman". - Attila Csordas
Gary Becker (economics) blogs. And, as I write in the comments on Martin's blog, at least three Fields medallists blog (Terry Tao, Tim Gowers, and Alain Connes). The Fields medal is a much more exclusive prize than the Nobel - I'm guessing about 10 percent of the living Fields' medallists blog! Not sure why prominent mathematicians are so much more likely to blog than people in other areas. - Michael Nielsen
Economists do tend to blog don't they. Not quite at a Nobel level, but you can add Tyler Cowen, Alex Tabarrok, Dani Rodrik, etc to that list as well. - Deepak
Somebody loves us at GT: "Time to get psyched — and sign up! BioBarCamp is a mere three weeks away, and there are only 45 people registered to attend, with room for 55 more. At Pimm Attila Chordash lists all the attendees so far, including some from the systems biology community of scientist bloggers like Pedro Beltrao, Jason Bobe, Cameron Neylon, Deepak Singh, Ricardo Vidal, and Andrew Yates." - Attila Csordas
Did you know that you are part of the 'systems biology community of scientist bloggers'? - Attila Csordas
Should there be a field of systems blogging? :) No-one's ever called me a systems biologist before... - Cameron Neylon
Is there a central resource/recommendation list for finding accomodation etc nearby? I'm not sure I can make it but I'd like to scope out possibilities (with, as you can see, minimal effort on my part :-) ). - Bill Hooker
"Personal genetic knowledge is sort of like knowing your blood type: Important to know but far from sufficient." Depak already hunted down this post: http://is.gd/Spz - Attila Csordas via Bookmarklet
It's funny to see how this Wired founder, Kevin Kelly and fellows like him (Tim O'Reilly) are finally paying a big chunk of attention to biology due to personalized genetics. We should come up with The Biotech Geek Guide in time! - Attila Csordas
Kelly is a longtime fan - he wrote a book with biological ideas at its heart about 15 years ago. "Out of Control" - well worth reading. - Michael Nielsen
You are right about Kelly, I knew about that book, just ignored. - Attila Csordas
If memory serves, I think Aldhous Huxley and H G Wells explored some of these ideas, too, in fictional settings. - Maxine
I invited Kelly to BioBarCamp, he knows IFTF well. - Attila Csordas
May I like stuff on which I hardly have any idea?: "An algorithm is presented for graphics processing units (GPUs), which execute single-precision arithmetic much faster than commodity microprocessors (CPUs), to calculate the exchange-correlation term in ab initio density functional calculations" - Attila Csordas
One of the cooler things I got a chance to see was a GRAPE card running all the force calculations for MD, and then interacting with the actual simulation using a haptic joystick. Too cool!!! - Deepak
say at the end of every session there is some time for 1-2 web based questions. I don't expect a big online audience but that's not the point. The point is to make it possible but I cannot guarantee this right now. - Attila Csordas
might be logistically hard, but any plans to post session videos on youtube after? I suspect a lot of people are interested, but just don't know about it - Daniel Kluesing
I would guess enough of us will be carrying web cams, key question will be connectivity and platforms. But it worked pretty well at the North Carolina Science Blogging meeting earlier this year. - Cameron Neylon
1 tricky thing about FF is that all forms of all my tweets are here and so you can see that I am a perfectionist and working on an inforich tweet a lot :) - Attila Csordas
Moshe Pritsker:"1) I put the word “basic” in BIG quotes because: is there anything in biology today that can be considered “basic”? Biological research is becoming more and more fragmented, and researchers become more and more focused on their specific areas. Typically, as I observed in many labs, a neurobiologist would not know how to do a Western blot, and a biochemist would not know how to perform a simple cell staining. These are very “basic” techniques." - Attila Csordas via Bookmarklet
True, Attila. It's always been hard for scientists from different fields to communicate on the same level. - Mr. Gunn
"Bowie is marvelous as Tesla, who appears as a quiet, calm genius, one all-too painfully aware of the dangers of obsession.
For that matter, most of the cast is truly top notch. Particularly, Bale and Caine, reteaming with their Batman Begins director, Christopher Nolan. Jackman also delivers great performances as both Angier and his drunken doppelganger.
Surprisingly, the weakest link in this magic trick is Scarlett Johansson as Olivia, the lovely assistant who serves both Borden and Angier on stage and at home. Normally a solid performer who’s comfortable in foreign territory (as in Girl with a Pearl Earring and Scoop), she seems a little out of place amidst the fine-tuned talent of her cast mates; her faux British accent frequently does its own disappearing act. That’s not to say she’s terrible, but she has done better." - Attila Csordas via Bookmarklet
I liked the movie. I actually like the Illusionist better for some reason. Scarlett's accent is pretty bad isn't it :) - Deepak
Haven't seen the Illusionist yet, problem is that don't really like Edward Norton. But will watch it. - Attila Csordas
Bale and especially Nolan are both extremely gifted in their respective lines of work. Can't wait for Dark Knight. - Daniel Jurczak
And I haven't seen the American Psycho yet (just some scene at HBO) which made Bale famous. - Attila Csordas
"Most important, the future of open access probably does not lie in journal publishing models. The huge success of online literature databases such as arXiv (http://arxiv.org), free to publish and access, is significant. Such databases currently host mostly non-peer-reviewed preprints, and so are of little value for career building. But academic organizations throughout the world could, if they wished, build an equivalent archive of peer-reviewed papers." - Attila Csordas via Bookmarklet
Tedious -
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nature.com > Journal home > Table of Contents - Graham Steel
This is a very short Correspondence letter in Nature that itself is a comment on an earlier Correspondence letter. I will post the whole thing on Nautilus blog at some point when I have some time (as I did the earlier letter). I tend to post the full text of Correspondence letters and other bits of short journal content, when they are published, that relate to authorship on that blog, if you are interested. Today, for example, there is a brief news item up there. - Maxine
PS whatever one's opinion of the letter itself, the title isn't useful. Attila's extract is basically the writer's point. - Maxine
I'll need to go back through the correspondence but, putting aside the fact that arXiv is not free, the extract as quoted seems to be based on the idea that peer review can be carried out for free. The 'journal model' is not what costs money; its the peer review process and the brand management associated with it. Financially viable Open Access publication would clearly benefit from (I still don't agree it requires) cheaper modes of peer review. And we still haven't really worked out how to do it. - Cameron Neylon
Going back to the earlier letter and the main body of the response which is about third world access. I think the first letter makes a good point. Access for third world scientists is a compelling argument for OA but a strict author pays model is clearly not consistent with this. What I found interesting talking to some scientists is that even if they can get the fee waived they find having to ask this embarrassing and even the comments that they can to be paternalistic. There is more to it than just money. - Cameron Neylon
I am shocked how underutilized the undergrads are at mostly-graduate institutions. They're like a second class. I went to a PUI, and we weren't treated as menial labor there. - Donnie Berkholz
This was discussed here sometime ago when someone linked to a PR article that appeared online. - PauloNuin
Here's the structural proteomics example I mentioned previously: http://www.nature.com/nsmb/jou.... "All cloning and initial expression, purification and HSQC/crystal screens were performed at the Ontario Cancer Institute (OCI) over a 12 month period by A.D., D.C. & A.Y. with the help of one FTE technician and (for 4 months) six summer students". - Neil Saunders
On the topic of under-utilisation: we once had a plan to set up something like Condor on machines in the undergraduate computer labs, for number-crunching during vacation. Faculty IT was not impressed, naturally :) - Neil Saunders
I know the people that published the Nature Structural Biology paper. - PauloNuin
"I read recently about the cease and desist letters sent to 23andme and other personal genomics companies selling tests directly to consumers. 23andme has responded, saying that they agree with the ultimate need for regulation, but that harnessing the consumer internet for personal genomics is a really valuable scientific tool.
I have to say I find myself doubtful about the urgency of this regulatory move. It smacks more of the hand of the AMA, an entrenched industry trying to make sure that the new tools of genetic testing remain under the thumb of doctors, than of true consumer protection. You have only to walk into Whole Foods to encounter a multi-billion dollar industry of supplements making all kinds of dubious health claims, which is completely unregulated. Why pick on personalized medicine, which has way more substance, and at least so far, way more care in the types of claims it makes?" - Attila Csordas via Bookmarklet
"Welcome to the first installation of Hourglass, a blog carnival devoted to the biology of aging. This first issue corresponds with the second blogiversary of Ouroboros, but mostly I consider it a celebration of the excellent (and growing) community of bloggers who are writing about biogerontology, lifespan extension technologies, and aging in general.
Without further ado, then, let’s get started:" - Attila Csordas via Bookmarklet
UniProt is one of the first life sciences databases to distribute all of their data in RDF format (both via FTP and the Web, ~1B triples) -- that ought to count for something :-) - Eric Jain
For my money, OBO is trying to do semantic web in a big ambitious way, some success already but still a long way to go http://www.obofoundry.org/ - Duncan Hull
WormBase - one of the first model organism databases - is in the middle of a ground up rearchitecture that embraces (some) semantic web principles. All vapor ware at this point but I hope to have a public test site available soon. - Todd Harris
Also, if I remember correctly, EColiHub is also planning an RDF backend (I could be wrong) - Deepak
Agree that OBO are trying to do good stuff with OWL, etc. I think SBML is impressive too. So semantic web == RDF ? If it were that easy, every web service would emit it :) - Neil Saunders
IMO RDF is a sufficient condition for an application to be considered SemWeb. In the end it's a representation of a graph, which is what the SemWeb is all about. Ideally RDF with a SPARQL end point. That's pretty much what the Talis platform offers. OWL is a part of the SemWeb stack, but you don't always have to define a vocabulary. - Deepak
Semantic web (as defined by the W3C) != speaking toasters. It's "just" data (RDF/OWL) that is accessible on the Web. Bonus: Provide a SPARQL endpoint so people can query the data rather than just retrieve it by URI. Challenges: Data modeling, scalability (if you have a lot of data), and creating generic-yet-usable end user tools that work directly with the RDF graph data model (I have yet to see any of these)... - Eric Jain
"generic-yet-usable" you hit the nail on the head :) - Deepak
RDF, OWL, OBO, SPARQL endpoints WHATEVER, doesn't really matter. One of the most important things is agreeing on, defining and sharing vocabularies. Easy to say, much harder to actually do. Despite all the semantic web hot air daydreaming, there aren't actually that many people actually doing it. - Duncan Hull
Some of the Semantic Web standards and tools may be useful for defining and sharing vocabularies, but where they really shine (and stop being overkill) is when you realize that you won't ever agree on one true shared vocabulary, but still need to be able to map/relate concepts from different vocabularies. That, and the generic, graph-based data model is kind of neat :-) - Eric Jain
Thanks folks for giving a little homework for the poor experimental scientist. :) - Attila Csordas
"HealthMap goes beyond the standard mashup and is more like a small-scale implementation of the long-awaited semantic web. The site, which the researchers describe in the latest issue of open access PLoS Medicine, creates machine-readable public health information from the text indexed by Google News, World Health Organization updates and online listserv discussions." - Attila Csordas via Bookmarklet
Nobody on Google even has that last name - it just seems to be a word. But there are only about ten people with my last name on Google (and one of them is a hostel in Singapore), so I shouldn't judge people's unconventional names. - Eva
I seriously don't judge anyone's unconventional names, Eva. :) I just want to collect a little information on BioBarCampers in advance as sharing it could be good for all of us when meeting to each other. This is part of my "polite and symmetrical unconference information trade" strategy based on my previous Camp experiences. - Attila Csordas
I know. And I always think it's weird when people are not on Google, even though *most* people aren't. (I tried to Google my whole high school graduation class once. Only about ten are there. I'm sure the other 30 exist somewhere.) - Eva
even more - disappointing but also interesting - to Google one's own parents and earlier generations. For my father I only found so far, 3 results or something although he wrote some books. - Attila Csordas
