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Shiran Pasternak › Comments
Would you call DAS a communication protocol or a data format? (http://biodas.org/documen...)
Pierre Lindenbaum and Deepak Singh liked this
It's not a protocol in my book
- Deepak Singh
from iPhone
False choice. Calling it a "service" might be more fitting (it has both a protocol and a data format).
- Shiran Pasternak
Shiran, then you would say DAS (service) = HTTP/SOAP (protocol) + XML (format)?
- Andrew Su
That's pretty much what all web services are aren't they? REST/SOAP + XML/JSON
- Deepak Singh
DAS is a layer on top of these standards. The protocol describes how a client defines object types (e.g., genes) and coordinate slices; The data format describes how the results are represented in XML.
- Shiran Pasternak
@Shiron does DAS really defines what is the type of object ? I mean, is "gene" a simple word or is it a component of an ontology ?
- Pierre Lindenbaum
@Pierre DAS only defines "feature" as a type. There is no sequence ontology (not last time I looked). But it's up to the provider to define the interface so that a client can request meaningful objects like "genes" (or "pierres," for all it cares).
- Shiran Pasternak
thanks
- Pierre Lindenbaum
thanks all for the comments. Personally I think this is largely semantics, but I suppose if we talk about it in a paper the semantics should be right...
- Andrew Su
What problems does Google Wave solve? - http://news.ycombinator.com/item...
Daniel Mietchen, Iván Abrego, Larry Hawes and 3 other people liked this
"I haven't bought into Wave yet, although it has more to do with the current UI than anything else. In addition to what's mentioned above, there are plugins for LaTeX, for rendering molecules, etc which make collaborative editing very powerful, potentially at least."
- Deepak Singh
I'm still not convinced by wave (slow, messy, ... ) but ok, it is still beta. However, I found this comment interesting ( http://www.slate.com/id... ) : "The core feature of Wave is that it is a real time communication PROTOCOL. Right now that manifests itself as live time chatting, but Wave is not meant to be just a fancy new IM client like you seem to have been using...
more...
- Pierre Lindenbaum
I am still not convinced either, but the Slate article is right. The problem is the current implementation. Everytime I see it, my reaction is, put some of those features into Etherpad and you have one powerful system. Wave is not an application, so we shouldn't be thinking of it as one, at least in the long term
- Deepak Singh
I haven't bought into Wave yet either, although I'm hoping I will at some stage. I suspect that will be when Wave becomes interesting by slinging data rather than just text around. A new form of bibliographic manager or universal blog commenting system is a lot more interesting than a new slant on email.
- AJCann
Wave is very promising and interesting, but I think it will be a couple of years until it matures into a truly useful platform. I'm not giving up on email and wikis for collaboration just yet.
- Matt Leifer
Wave is really useful in its current incarnation for collaborative editing of structured documents a la wikis. For free-form discussion a la IM, Twitter, or FriendFeed, not so much; at least not currently.
- Shiran Pasternak
Keep your competition from doing real science?
- Egon Willighagen
Could we have a list of google wave names somewhere so that I can figure out what Life-Scientists are on there?
Jeannette Høvring, Daniel Jurczak, Jason Winget and 20 other people liked this
toddwharris@googlewave.com
- Todd Harris
just added you to Life Scientists wave
- Cameron Neylon
from twhirl
A Google Wave might be appropriate for tracking such a group.
- Shiran Pasternak
shiranpasternak at the same domain.
- Shiran Pasternak
search "with:public research" and you will find the "Research collaborations in Wave" wave endre.sebestyen@googlewave.com
- Endre Sebestyen
yann.abraham@googlewave.com
- Yann Abraham
Searching Google Wave with "tag:the-life-scientists" will get you to "Research collaborations in Wave", a good starting point for life scientists.
- Martin Fenner
b.brembs@googlewave.com
- Björn Brembs
mndoci
- Deepak Singh
I also missed out on the invites .. if anyone knows someone .. :)
- Pedro Beltrao
I'm firstname.lastname
- Ruchira S. Datta
firstname.lastname here too
- Andrew Clegg
I don't get how you search in public waves. I've tried searching for tag:the-life-scientists and it gets no hits -- I think it's just searching my own waves
- Andrew Clegg
there was a thread by Kol about wave usernames couldn't find the link
- ffcode
Aha -- with:public . They really should include a button for that
- Andrew Clegg
anna.k.croft
- Anna Croft
Lots here: http://ff.im/91NZC
- Kol Tregaskes
thanks Kol
- ffcode
attilacsordas
- Attila Csordas
I never got invited to the party :(
- Lars Juhl Jensen
AndrewJamesPerry
- Andrew Perry
avijitguharoy@googlewave.com
- A Roy
allyson.lurena@googlewave.com
- Allyson Lister
@Endre: You can link to waves, eg: https://wave.google.com/wave...
- Nick Lothian
mbembee@googlewave.com
- embee
000.cacarr@googlewave.com
- Christopher A Carr
cassjohnston
- Cass Johnston
plindenbaum
- Pierre Lindenbaum
firstname.lastname också
- Egon Willighagen
diegomorelli76@googlevave.com
- diego morelli
abhishek.twr@googlevave.com
- Abhishek Tiwari
Would like to be added to life scientists wave, please! david.rothman@googlewave.com
- David Rothman (☤)
@David: done
- Pierre Lindenbaum
Many thanks, Pierre. :)
- David Rothman (☤)
churchsg
- Sally Church
life scientists wave: me too, thx
- Attila Csordas
Count me in: matt.j.wood
- Matt Wood
jeanclaude.bradley at googlewave dot com
- Jean-Claude Bradley
chrisamiller@googlewave.com
- Chris Miller
inspiring2designllc@googlewave.com
- Justin H. Johnson
somebody please add me too attilacsordasat...
- Attila Csordas
Attila: can't seem to find attilacsordas@googlewave.com.
- Shiran Pasternak
it does exist I can tell ya :)
- Attila Csordas
@Attila: tried a different way... yer in.
- Shiran Pasternak
An undergraduate student in our lab, Caleb, just got his wave invite. I told him to look at this thread for possible people to connect with.
- Steve Koch
+1 skhadar@googlewave.com
- Khader Shameer
got it, thanks
- Attila Csordas
murvine - thanks!
- Christopher Murvine
Afternoon all. I've written my first robot, which hopefully will embed an interactive mass spectrum into a blip whenever a UniProt name is encountered in the text, and corresponding mass spec data is found for this protein. I say "hopefully", as I've not been able to test it for real, as, alas, I have no account. When are the next batches released? If it's not for ages, does anyone fancy testing it anyway?
- Neil Swainston
Am now Waving as ben.blackburne.
- Ben Blackburne
Now waving as lars.juhl.jensen
- Lars Juhl Jensen
waving too: sciphu@googlewave.com
- Nils Reinton
waving as fgibson
- Frank
aemonten@googlewave.com. How can I get started with the life scientists wave?
- Alejandro Montenegro
my wave ID: macmanes@googlewave.com
- Matthew MacManes
dan.swan@googlewave.com searching is sloooooow trying to find the life scientists wave right now!
- Daniel Swan
chris.lasher@googlewave.com
- Chris Lasher
sjcockell@googlewave.com
- Simon Cockell
jwhabig@googlewave.com - Jeff Habig
- Jeff Habig
comprendia[at]googlewave[dot]com Mary Canady
- Mary Canady
rebeldad@googlewave.com Brian Reid (PR guy for life science types ... I promise to behave)
- Brian Reid
bronxman
- Jack H. Pincus
I'm trying to get a Solexa/Illumina Sequencing Wave going. Search "with:public Illumina" or add me macmanes@googlewave.com
- Matthew MacManes
waving as georgkam
- george
For some reason, I'm stevekoch3 but glad to finally have a preview account!
- Steve Koch
And I found the research collaborations wave by the following search: "with:public tag:the-life-scientists"
- Steve Koch
mine is pedrobeltrao@googlewave.com (thanks to Mr Gunn)
- Pedro Beltrao
In case there is still someone with spare invitations: piotr.byzia at gmail.com
- Piotr Byzia
tom.sante@googlewave.com
- Tom
Im steelgraham7@googlewave.com
- Graham Steel
sametstalker@gmail.com
- Samet Güngören
michael.kuhn
- Michael Kuhn
Requesting for life scientists wave, abhishek.twr@googlevave.com thanks in advance
- Abhishek Tiwari
The usual, neilfws.
- Neil Saunders
now that I am finally on board: danjurczak@googlewave.com
- Daniel Jurczak
i'm mightyfib(at)gogglewave(dot)com Your most welcome to add me...:O)
- Jeannette Høvring
mine is dave.lunt
- Dave Lunt
michael.chelen@googlewave.com or @gmail.com can't see any way to check :D
- Mike Chelen
is there any good way to import contacts? it seems to work through the google contacts system like gmail
- Mike Chelen
pengwen.not.penguin@googlewave.com
- Parvez Halim
Hadoop for Bioinformatics - http://www.slideshare.net/mndoci...
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Christopher Fields, Justin H. Johnson, Endre Sebestyen and 16 other people liked this
More "like"ing you gave a talk on this. Slides are very contextual, rather than textual, so I don't think many will get but the gist of what was going on. I can certainly guess, though. Also, some of these look familiar. Like that you still have the computer with the password written on it (from Matt Wood, right?). Hope they changed the password by now.
- Chris Lasher
Deepak, is there a way to listen to your speech ?
- Pierre Lindenbaum
Cloudera is working on putting up videos of all the talks from the conference, but didn't give an ETA. Chris, you're right: the slides don't do the talk justice. They go very well with the delivery. Seeing the phrase 'c. elegans' in a purely software conference gets me as excited as seeing a word like 'Java' in a bioscience conference.
- Shiran Pasternak
Video should be up soon. Got great feedback from the attendees and on Twitter. Next place to talk about this stuff - Supercomputing
- Deepak Singh
wonder how the ideas displayed on 41 and on 104 will develop together :-)
- Claudia Koltzenburg
me too :)
- Deepak Singh
Version numbers should be boring - http://www.dagolden.com/index...
Unfortunate yet well-written treatise on versioning in Perl. Really?? Really? Don't I have enough to worry about?
- Shiran Pasternak
The Onion Publisher T. Herman Zweibel: ‘Well, I’ve Sold the Paper to the Chinese’ - http://www.theonion.com/content...
BTW, Zweibel is Yiddish for "onion"
- Shiran Pasternak
The Geography of Jobs - TIP Strategies - http://tipstrategies.com/archive...
I'm not that impressed with map-overlaid bubble charts but this animation tells a good story.
- Shiran Pasternak
Bless the Cyclist, on Your Left! - City Room Blog - NYTimes.com - http://cityroom.blogs.nytimes.com/2009...
Forgive me father, for I have spinned.
- Shiran Pasternak
Zappos Maps Sales in Real-time - http://flowingdata.com/2009...
This is brave. What's next, real-time earnings reports?
- Shiran Pasternak
Rappin’ for Science - TierneyLab Blog - NYTimes.com - http://tierneylab.blogs.nytimes.com/2009...
This vid is hox, yo.
- Shiran Pasternak
The good and bad of genome viewers - http://saaientist.blogspot.com/2009...
Interesting take, but still too "one-dimensional" in my opinion. If genomes are not linear, then should they be drawn left-to-right at all?
- Shiran Pasternak
Visualizing Twitter as Barack Obama Became the 44th President - http://flowingdata.com/2009...
Reminds me of that scene from Close Encounters. You know. That scene.
- Shiran Pasternak
Op-Ed Contributor - Oaf of Office - NYTimes.com - http://www.nytimes.com/glogin...
I'm excited to proudly and grammatically reclaim my split infinitives.
- Shiran Pasternak
Search Without Effort: The Quick Search Box - http://googlemac.blogspot.com/2009...
Sounds like the replacement for Quicksilver. Developed by alc0r, creator of Quicksilver, the best Mac app ever.
- Shiran Pasternak
diamonddave - http://www.thetyser.com/
Woohoooyeah!
- Shiran Pasternak
The year 2008 in photographs (part 1 of 3) - http://www.boston.com/bigpict...
Jaw-dropping images.
- Shiran Pasternak
what is the size of the longest chromosome ?
Ahmet Yukselturk and Chris Lasher liked this
Human C'some 1 is 247,249,719bps - don't know about other organisms (http://is.gd/cjUu)
- Simon Cockell
wheat 3B is ~ 995 Mbp
- Neil Saunders
Nearly 1 billion base pairs? That's huge! [Preemptive "That's what she said."]
- Chris Lasher
1 billion base pairs and imagine 4 or 5 copies of that in the same nucleus!
- Paulo Nuin
Imagine the poor guys genotyping those organisms :-)
- Pierre Lindenbaum
You mean rich guys, right? They need a ton of money if they want to sequence it.
- Paulo Nuin
Wheat is not being sequenced yet; For maize, I can say, it's a total pain: not because of its length (2.5 Gbp), but because of its repetitiveness (75% of it is transposable elements).
- Shiran Pasternak
I mean: most (all?) of the methods are based on the fact that the organisms are duploid
- Pierre Lindenbaum
Yes, but still they are very large chromosomes, and as Shiran pointed out, very repetitive.
- Paulo Nuin
@Shiran 75% TEs? Is it known why there's such a high percentage in maize, or is this one of those mysteries currently under investigation?
- Chris Lasher
15dec2008 5.53pm: second daughter arrived. Ayko Aerts. 2.9kg
Congratulations Jan!
- Pawel Szczesny
Congrats, Jan. My first daughter just arrived on Dec 12.
- Shiran Pasternak
@jandot what do you mean by 'indexed' flat file ?
Don't know exactly myself. I believe where each line is identified by an index? I've got >6million lines in a file where first column is basepair position (ordered from small to large). I want to be able to very quickly extract a chunk of the data (i.e. part of a chromosome). Although I'm all for databases they can become very slow at this point. From what I understand (and what mza has told me) indexed files should be much faster for this.
- Jan Aerts
Note sure i it can fulfill your needs: have look a Oracle/BerkeleyDB
- Pierre Lindenbaum
you mean something similar to a Nexus file, where the information is broken into blocks?
- Paulo Nuin
With nexus you have to define the blocks beforehand, isn't it? What I need is on the fly quick search. I actually think that it's so that I can use binary search for example.
- Jan Aerts
Yes, with Nexus you would need the blocks predefined, but your parsing will be fast if you have a short list of possible blocks.
- Paulo Nuin
Binary Searches: use the berkeley API : http://www.oracle.com/technol...
- Pierre Lindenbaum
Also just found http://0xcc.net/ruby-bsearch/
- Jan Aerts
SRS worked by indexing flat files for years - don't know about now - but there must be a paper out there somewhere.
- Allyson Lister
Jan your bseach algorithm seems to only work with data in memory. An alternative to search a big dataset using binary_search/lower_bound/upper_bound would be to build a (binary) file of your data (where all records have the same size) and scan the file using a random acces strategy.
- Pierre Lindenbaum
Why not create an index by noting file positions for say certain base pair positions. If you're working in C you could simple fseek to that position, based on a binary search of the indexed values. Very crude and it seems a DB would be a much better solution
- Rajarshi Guha
Check out http://www.hdfgroup.org/HDF5/T.... We're considering that for short read indexing.
- Shiran Pasternak
Visualize or summarize? - http://saaientist.blogspot.com/2008...
Mike Chelen, Patricia F. Anderson, Khader Shameer and 7 other people liked this
Nice. While I like and appreicate good visualizations, there are too many cases (networks are my current bug bea), where it seems that the goal is just to make pretty pictures. In those cases, it has seemed to me that unless I know what I'm looking for, the visualization is worse than a summary (for practical purposes). Of course a combination of vis and summary is ideal.
- Rajarshi Guha
Man, great thinking for a very often occuring problem !
- joergkurtwegner
I'm not sure how much Processing can help with ad hoc data visualization. There is still a learning and programmatic curve, albeit smaller. How can you easily load the data and provide a graphical UI to it? I played around with Spotfire a few years ago, which can readily transform any tabular data into particle plots and other agnostic yet intuitive visualizations. But Spotfire is super-expensive. Google and NYTimes are taking steps towards providing open visualization APIs.
- Shiran Pasternak
I agree, I quickly looked into 'processing', and for my daily work I could not imagine to work without SpotFire, but I can ignore 'processing'. Beside, the interface in 'processing' seems not practical and flexible enough for scientific data ?
- joergkurtwegner
@Shiran: "not sure how much Processing can help with ad hoc visualization". That's _exactly_ what I use it for. The scripts are often so small that they are merely "sketches" (in Processing-lingo). Even though a tool like Spotfire is very useful, it falls short when your data contains many types of information. For example: clone read pairs mapped on a genome: there are the actual mappings, whether or not they map where they should, quality values, inversions, ... Any visualization has to be custom.
- Jan Aerts
In that case, do you have any example scripts you can share? I didn't mean to rag on Processing. It's a great tool (especially coming from a Java and OpenGL background), and the applications out there that use it are fascinating.
- Shiran Pasternak
Jan I'd also be interested in some examples. The one and only processing sketch I've attempted is http://tinyurl.com/5r7543 to demonstrate a simple algorithm. When visualizing data I tend towards plots and molecular graphics. There's also ruby-processing http://github.com/jashken... which you might find easier as a ruby programmer.
- Adam Kraut
@Shiran, Adam: As they're sketches of current work, am not allowed to put them online. But I will probably generalize one of my current visualizations and put it on github. Will let you know when that has happened. My very first hack was a proof-of-concept for comparative map viewer (http://tinyurl.com/5gkt85).
- Jan Aerts
It is so cool to see Processing used to display scientific data! It can really lead to wider usage of advanced open source data vis libraries and APIs, that includes Google, NYT, and others. Check out the Javascript Processing.js which nicely expands the cross platform compatibility. If you get a chance to put more examples on github it would be appreciated, looking forward to seeing what else you are working on =)
- Mike Chelen
A simple, fast, and accurate method of phylogenomic inference - http://genomebiology.com/2008...
Open access paper by Martin Wu and Jonathan Eisen on phylogenomic inference
- Shiran Pasternak
Re: Security vs.Volatility... - http://jer979.blogspot.com/2008...
"I totally understand that for many situations (such as self-employment) it's necessary at certain times to shift accounts and rebalance cash reserves. But if cash is not urgently needed on hand, disciplined investing can pay off. Even though we're currently in a down-market, we hope that the market will return. Incremental contributions to investment accounts result in dollar-cost averaging, which in turn offsets volatility."
- Shiran Pasternak
Re: Designing potent posters: Process, Format, Presentation - http://thewildtype.com/2008...
"Great post. I'll take your challenge. For my next meeting (International Professional Poster Printers Conference, held in Kathmandu), I'm going to go back to basics and use a modularized poster. This is part of what I think is a grassroots effort to reclaim our focus and our creativity. It's very reminiscent of the Paper Web. Enthusiastic about my work? Now that's a whole other issue."
- Shiran Pasternak
Toilet - paper researchers create 3 - ply tissue - NYTimes.com - http://www.nytimes.com/aponlin...
Finally! Yes!
- Shiran Pasternak
A level playing field? : Article : Nature - http://www.nature.com/nature...
Nature "weighs in" on doping in sports. Money line: "The anti-doping authorities have fostered a sporting culture of suspicion, secrecy and fear."
- Shiran Pasternak
Unstressed - http://www.guardian.co.uk/media...
The referenced rant is a gem
- Shiran Pasternak
Brains on the Line - http://benfry.com/writing...
Gee, Todd is such a swell guy
- Shiran Pasternak
Life’s Modest Majesty - http://blogs.discovermagazine.com/loom...
Ticks me off when alarmists cite this so-called "extinction rate," without acknowledging a species "emergence rate." After all, evolution didn't stop with the Industrial Revolution. Not sure if the study includes data over the last 50-100 years, but overall it shows an interesting trend.
- Shiran Pasternak
Ron Mueck: Hyper-Realist Sculptor - http://paintalicious.org/2007...
Saw this exhibit at the Brooklyn Museum
- Shiran Pasternak
Airfare Watchdog - http://www.airfarewatchdog.com/
Manual tracking of last minute airfare deals. If you're not too particular and can travel on a whim, this is ideal.
- Shiran Pasternak
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