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Neil Swainston › Comments
One giant leap for Taverna: workflow: workflow construction workbench used by NASA's JPL in WS-infrastructure - http://www.omii.ac.uk/wiki...
Steve Koch, Pierre Lindenbaum, Pawel Szczesny and 2 other people liked this
"NASA’s Jet Propulsion Laboratory (JPL) created the first American satellite and are now using Taverna for their Web Services-based infrastructure.[..] One of the challenges faced by the research team is the integration of various models that are used to explore the science behind the JPL’s missions. These models have been developed independently and run on different platforms, so their integration is not straightforward. The JPL’s solution is to wrap each model as a Web Service and drive them with a Web Services-enabled workflow." [From the OMII-UK newsletter: http://www.omii.ac.uk/wiki...]
- 'Mummi' Thorisson
?!?
- Neil Swainston
Rocket Science?
- Duncan Hull
Has our quest for completeness made things too complicated? - http://nsaunders.wordpress.com/2009...
Marcos de Carvalho, Brad Chapman, Michael Nielsen and 31 other people liked this
Neil, great post. And you're right, we do make things too complicated sometimes, but do we do that at the level at which we ask questions, or at the software implementation level? My take is the latter, cause you need to ask questions the way you want to, but that doesn't mean what makes it all come together has to be one complex mess
- Deepak Singh
Glad you like it. One of those that bubbled up out of frustration at inability to achieve! I feel that science is the business of turning complex (real-world) things into simple models - and that we've moved away from that idea.
- Neil Saunders
I'm a sucker for this kind of ambitious thinking. Go Neil!
- Bill Hooker
I think it's a good sign that things like this are now obvious. Things start out as a complex mess of disconnected things, overlapping complicated ways of connecting them are devised, then it becomes obvious what the simpler thing to do is.
- Mr. Gunn
Great ! But aren't you re-inventing something like RDF Neil ? feature/probe/value is nothing but a RDF statement...
- Pierre Lindenbaum
No, I don't want to reinvent anything. If RDF will work for me, I'll use it. I'll also use SQL, NoSQL, key-value pairs, document-oriented or whatever it takes. I just think that trying to integrate data by combining other peoples large, complex representations is not working. We need to simplify the whole business.
- Neil Saunders
I think there is a middle road here - we need high level generic descriptions like what Neil is proposing (and like my "We have stuff, we do stuff to it, which makes stuff"), but also a way of pointing to more sophisticated information that might be useful in specific contexts. I think we can have the best of both worlds as long as the data representation is separated from the metadata and the organization of each can be described in a machine readable (and agreed!) form
- Cameron Neylon
I'm too old school, leaving comments on blogs... who does that any more. I’m sure you’re aware that you’ve just described a model using *triples*. Which means you could start storing these kinds of simple relationships in a triple store like virtuoso etc. As you say, you don't have to reinvent anything, just simplify the use (conventions) of existing approaches (e.g. RDF). I would like...
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- Greg Tyrelle
@Greg about the web interface, one cool interface for adding RDF statements/triples is freebase/Acre: http://www.freebase.com/apps/
- Pierre Lindenbaum
I like blog comments :-) Yes, my example looks like RDF triples. No, that was not really my intention. Let's ask these questions: (1) what data relationships would make sense to a biologist? (2) what are the commonalities in the data, which a biologist may not have considered at an abstract level? As I wrote in the post, many datasets that look different are really different ways of looking at the same thing.
- Neil Saunders
The joys of data modelling :-) For (1): I'm afraid asking for a definition of some data relationships is building an(other?)) ontology.
- Pierre Lindenbaum
Let's put it another way. What we have, presently, are quite complete, often large and complex, but useful and usable descriptions of individual experiment types. "Integration" essentially means "parse them individually and mash-up the results". That's what makes it difficult. Perhaps we need an "ontology of integration" :-) But let's keep it really, really minimal.
- Neil Saunders
I actually think you will struggle to find data commonalities across bioscience. Even the simple proposal of target, measurement, value could break down in many cases e.g. we tried ages ago to get some intensity data from a bunch of microarray experiments and we gave up because we couldn't get across what we needed. What are you really measuring? Does it mean the same thing to different...
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- Cameron Neylon
I think there's a good case for storing, in the first instance, raw values. Figure out how to process them later (that's statistics). Focus on trends (up, down, stayed the same). Focus on well-defined variables that do mean the same to everyone (intensity, in theory = amount of transcript, regardless of the very real difficulties). And I think more experiments fall into...
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- Neil Saunders
@Pierre freebase is exactly what I had in mind, however the web client (the best part) is not open. @Neil Store the data first, ask questions later. Nice. One of my hopes for semantic web technology was that is could be come a universal mashup system (RDF+ontologies+triplestores). But you start down that path, and you suddenly realise that the semweb is asking you to get your data...
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- Greg Tyrelle
But for me your example of a gel isn't raw data. The raw data is the image. Which might have several targets or assays on it. Up/down stayed the same is only really of interest in particular types of science. And I challenge you to find any well defined variables :-) Intensity to me is a measure of optical density but questions of background, object size, masking, averaging algorithm...
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- Cameron Neylon
from twhirl
But agree with what you and Greg are saying, first thing get the data somewhere, with allt the metadata you can automatically collect. Then worry about capturing more metadata as people do stuff with the data. Writing this grant proposal right at the moment.
- Cameron Neylon
from twhirl
And in microarrays, "raw" data is the image of the slide. But aside from a cursory inspection to ensure that it isn't complete rubbish, nobody much cares about that. I'd argue that there's a point in the preprocessing at which a numerical value emerges which could be called "useful" and which encapsulates the object being measured. It needs more work (e.g. normalization) to get information from it, but it's the "value" in feature/reporter/value.
- Neil Saunders
To me this about finding something a bit like an upper ontology that describes the general category that objects (targets, assay, value, inputs, outputs, data, process, sample) fall into. That lets you do the general integration, and the more detailed local data structures become more useful as you can agree more and more on what details are important. So I absolutely agree with what...
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- Cameron Neylon
Heh heh It was exactly that image that we did care about - which was the problem :-) I will admit to being an edge case, but in some ways we're all edge cases, they're just different edges...
- Cameron Neylon
Neil, may I link to this FF thread from Book of Trogool?
- D0r0th34
It's in a rough state but - http://dl.dropbox.com/u...
- Cameron Neylon
:-) Sure, different questions, different "levels" of data. I guess my angle is more a statistical one: how do I compare (seemingly) quite different datasets - what numbers can I extract and crunch? Less interested in the capture and description of data at every stage in the process.
- Neil Saunders
Dorothea, sure, not a problem.
- Neil Saunders
"This is a gel", "this is a sample",.... AFAIK all those kinds of statements are part of the OBI ontology: http://obi-ontology.org/page... e.g. "Agarose Gel" http://bioportal.bioontology.org/ajax_co...
- Pierre Lindenbaum
Sure, and those are very complete descriptions of experimental components. But what I want is: "I saw A on my gel, B in my LC/MS, C on my expression array and D on my SNP array and when I plug all that into some Bayesian predictor, it says cancer" :-)
- Neil Saunders
Ontologies are not the issue, it's more low level than that. I also work with microarrays, proteomics, metabolomics, and numerous physiological data sets. To keep all the data in one place I use a relational database, in this case postgresql because I like to store raw intensity values in array datatypes, along with pylons based web interfaces to display various views of the data to my...
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- Greg Tyrelle
My argument would be that the reason you're less productive is not because of the RDF and ontologies per se, but because the ontologies aren't really built for what we want to do. They're for describing certain types of outcomes, not for integrating data in a discovery phase. But Neil's (entity, probe, value) is still an ontology of sorts. It is just a higher level one. My belief is...
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- Cameron Neylon
But keep the discussion going - this is exactly the problem that e.g the SAGE project will have - http://sagebase.org - and as a notional member of the data working group I could do with all the ideas and help that's out there...
- Cameron Neylon
We are thinking too much in terms of data representation here. In the end what you are looking at is a data warehousing problem. You have different front end systems and you want to be able to pull data in for offline processing into a warehouse. That's pretty much what you do at any company doing a lot of analytics/business intelligence. Different types of data being collected in...
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- Deepak Singh
This reminds me of the type of approach we were considering a while back - with a focus on each observable event during an experiment. http://usefulchem.blogspot.com/2008...
- Jean-Claude Bradley
Neil, I was under the impression that normalization across arrays and labs wasn't actually a solved problem, yet. Surely that would have to come first before stripping things down to just assay-key-value?
- Mr. Gunn
Normalization ... aaargh! Most definitely not a solved problem
- Rajarshi Guha
Normalizing within your own experiments is hard enough, never mind across unrelated datasets. It's something we have to solve though, to make the most of public data.
- Neil Saunders
Neil, you may be intersted in looking at the Ontology-Based eXtensible Data Model (OBX) that was developed by Richard Scheuermann's group at UT Southwestern. It is being used for the ImmPort database (www.immport.org) The OBX model utilizes the BFO / OBI ontology as guides in creating a data model that is robust to new datatypes. You can see a presentation about it here:...
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- Burke Squires
Thanks Burke. ImmPort looks very impressive, I must say.
- Neil Saunders
This reminds me of what the TCGA is starting to do, by defining "data levels". For microarray data, Level 1 might be the raw images, Level 2, the intensity calls, Level 3, the normalized intensities, and Level 4 information on whether it's up or down regulated across multiple samples. For people like me, doing integrative analyses, it's easy to focus just on the higher level data and...
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- Chris Miller
which is exactly why you need separation of the layers and tools to bring data together for the downstream stuff
- Deepak Singh
from IM
Neil, I think you have just explained why tab-delimited files are often more useful than complex XML representations of the same data ;-)
- Lars Juhl Jensen
Tab-delimitted files would be grrrreat for me in my lab. If any of the rest of you would like to share our data, however, then you're completely screwed. Is the problem not that we're all duplicating each other's work by writing the same kind of parsers for the same kind of data? Proteomics (for example) has a standard (http://www.ebi.ac.uk/pride/). Is it really so hard to use / develop the community-based tools that are being generated around this standard?!?
- Neil Swainston
Well, the ratio of usable tools to schemas/ontologies is a whole other debate :-) But sure, in principle the tools are there - for individual types of data. What I highlight in the post is the difficulty of genuine data integration, as opposed to the current "write a parser for everything and mash it up" approach.
- Neil Saunders
#1 rule of data integration - if a format exists, it will be used
- Deepak Singh
...and if it doesn't exist there is a 70% chance someone will create it :-)
- Cameron Neylon
Chris M makes an important point wrt data levels, analogous to trace archives vs sequence dbs. Extending the sequence analogy, obsoleting levels will become important (it will rapidly become cheaper to resequence rather than store sequence).
- Chris Cotsapas
Let the internet replace scholarly journals http://www.theaustralian.com.au/higher-... (The Australian)
Duncan Hull, Jo Young, Sandeep Gautam and 6 other people liked this
Nice quote: "Academic publishing has a bizarre business model. Academics and scientists at government-funded universities and institutions carry out research and write papers about it. These papers are then reviewed by other state-funded scientists and handed to the editors of academic journals, who also happen to be on the government payroll. Funding for all the academics involved in...
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- Björn Brembs
Nice quote: "Academic publishing has a bizarre business model." Think that pretty much encapsulates it.
- Neil Swainston
Hey Elsevier, you listening? Mene mene tekel, assholes...
- Bill Hooker
EC:3.4.11.4 - http://lsrn.org/EC:3.4.11.4
Neil Swainston and Pierre Lindenbaum liked this
dereferencable identifier
- Egon Willighagen
Nice. Works for UniProt and ChEBI, too. Any chance of a web service equivalent?!?
- Neil Swainston
Yes, very likely... it's going to be integrated with sadiframework.org
- Egon Willighagen
Tailor-Made Mass Spec :The Scientist [2009-11-01] - http://www.the-scientist.com/article...
Tom Walsh and Neil Swainston liked this
Like the look of Decision Tree. Is it the hardware that needs improving or the software?
- Neil Swainston
♺ @genomepop: A google map for Biochemical Pathways: http://www.reportergene.com/2009... #bioinformatics
Pierre Lindenbaum liked this
NIcely done. However, still relies on navigating over static pathways (KEGG pathways at that). Upload SBML and auto-layout in SBGN facility, please... (Some people are never happy).
- Neil Swainston
Bioinformatics has made me very angry. I must light a candle.
'Mummi' Thorisson, Duncan Hull, Allyson Lister and Ruchira S. Datta liked this
what's it got you angry about? :)
- Allyson Lister
Bit of a private joke, I guess. One of the Profs here throw a right hissy fit in a meeting yesterday, said words to the above effect and then promptly lit a scented candle in the middle of the meeting to calm her nerves. I don't think I'm eccentric enough to get on in academia. (The anger with bioinformatics is just my general day-to-day demeanour.)
- Neil Swainston
That is - imaginative. Thanks for relating the story! :)
- Allyson Lister
@Neil I'm lighting a candle for you down in Hinxton ;-)
- Duncan Hull
how was it lit? via fire-breathing :)
- Frank
Passing on a question from a bioinformatics colleague who needs to put together lectures and practicals on systems biology: "Is there opensource/freely available software that can be used to carry out systems biology analysis?". Any information on existing teaching resources would be welcome...
Itachi, Mr. Gunn, Duncan Hull and 3 other people liked this
Try Copasi (http://www.copasi.org/) and JWS Online (http://jjj.biochem.sun.ac.za/).
- Neil Swainston
Thanks - they look useful.
- Noel O'Boyle
That's a tough question to answer. What specifically is he looking at? Pathways? Integrated analysis?
- Deepak Singh
If only it were possible to be specific - pinning down what exactly to cover in a systems biology course is part of the problem. The practicals will probably be limited by what is available and whether case studies or tutorials are provided (or are available on the web).
- Noel O'Boyle
+1 Deepak. Also http://www.sbml.org maintains a list of software compatible with SBML. Most of them are free / open source : http://sbml.org/SBML_So... http://sbml.org/SBML_So...
- Khader Shameer
Thanks Khader - that list looks very useful. Regarding the type of software, really anything from metabolomics analysis, microarray analysis, studying protein-protein interactions graphs would be useful. Again, the focus is on software for use in practicals (so should be easy to use, and free or open source).
- Noel O'Boyle
Bioconductor for microarray analysis, igraph for graph analysis, Cytoscape for visualization, network integration
- Rajarshi Guha
JWS Online (http://jjj.biochem.sun.ac.za/) is quite handy for teaching. The models are of a reasonably small size and it's web-enabled, so no faffing around with installs and what-not.
- Neil Swainston
Noel, you might want to redirect your colleague to http://sciencestack.com with this bioinformatics question.
- Jane Breezler
PathVisio / WikiPathways tool for creating and analysing biological pathway diagrams - http://www.pathvisio.org/
Ami Iida, Holly Rae, Daniel Mietchen and 8 other people liked this
I'd really like to see that refactored as a collaborative Google Wave gadget.
- Dan Hagon
Me too, re: Google Wave gadget. Then add SBML support, use SBGN in the display, support MIRIAM annotations and I can retire penniless.
- Neil Swainston
@Neil, there are a few other tools which support SBML and SBGN (see http://sbgn.org/Communi...). Wikipathways seem to be inventing yet another pathway format and dont provide a conversion to any other existing "standard". Shame as it would benefit everyone if they did.
- Frank
Thinking about it a little more, I'd really like to see the above refactored as a collaborative Google Wave Gadget. I've been involved in about five network reconstruction "jamborees" now, which involve flying loads of people around the World to sit in a room and discuss things that they could do with PathVisio (if it supported SBML...) or Payao. Anyways, this costs a fortune (see the...
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- Neil Swainston
@Neil: WikiPathways is intended exactly for that type of collaborative pathway creation. WikiPathways pathway format is based on, and developed in cooperation with, http://www.genmapp.org. So admittedly it's not a widely supported standard, but at least it wasn't a complete new invention. SBML / SBGN support is on its way. Re Google Wave: unfortunately, all this work predated Google Wave by several years...
- Martijn van Iersel
OK, I give in -anyone got a spare Wave invite for me? Thanks.
Carl Fulp, Mike Chelen, 'Mummi' Thorisson and 3 other people liked this
I'd be happy to receive an invite, too :-) thanks
- Claudia Koltzenburg
Oh is this where the Wave queue is? *stands in line*
- Bob O'Hara
No cutting in! :-)
- AJCann
Can I have your email address - please. I have 5 invites.
- Khader Shameer
steelgraham7 AT gmail DOT com
- Graham Steel
AJCann and Graham : both of you are invited. Got 4 more to share - pls send email address.
- Khader Shameer
Thanks Khader.
- AJCann
sent you a direct message w/ my email address
- Michael Kuhn
If anyone in Wave has spares can they also check the Life Scientists invite list? Drop me you're Wave address (I'm cameronneylon@googlewave.com) and I can add you
- Cameron Neylon
from twhirl
Khader or anyone nice, here's mine: ctt.journal at googlemail.com
- Claudia Koltzenburg
Khader, if you still have some, I am mikael dot huss at the same domain as Claudia above
- Mikael Huss
Hi Khader. neil.swainston_AT_manchester.ac.uk if there are any spares. Thanks.
- Neil Swainston
andrew.sid.lang AT gmail DOT com if you can - thanks!
- Jean-Claude Bradley
Send invites to Michael, Claudia and Huss. Sorry Neil and Bradley.
- Khader Shameer
that's ok Khader - we'll keep trying
- Jean-Claude Bradley
For the public record, I didn't receive a Wave invite from Khader :-(
- Graham Steel
Graham, that was a too early announcement :|, usually wave takes a day or two to send the invitation. In Wave's own words "Invitations will not be sent immediately. We have a lot of stamps to lick. "
- Khader Shameer
"usually wave takes a day or two to send the invitation" I was not aware of that, thanks for pointing this out, Khader. Thank you kindly for sending out the invites...
- Graham Steel
Yeah, See you on wave Graham :) !
- Khader Shameer
Thanks anyway, Khader.
- Neil Swainston
May as well add my name to the list of those left behind ! elbuono AT gmail DOT com
- Ian Simpson
from twhirl
still holding out - I know that if I get one of these, I'll get sucked into the Waveome and my thesis will soo *never* be done in time!
- 'Mummi' Thorisson
Got few more invites: added Ashish, Lucas, Andrew, Carl, Ian :)
- Khader Shameer
Mummi send me your gmail ID.
- Khader Shameer
We are the Robots. A first attempt at a proteomics robot for Google Wave. http://neilswainston.blogspot.com/2009...
Mackenzie Cowell, FedericaB., Joseph Jose and 12 other people liked this
Replied on the blog but will try to give this a go ASAP...but probably not today...
- Cameron Neylon
Hi Cameron. Can't make your Hackfest, I'm afraid, although I'd love to attend virtually if possible...
- Neil Swainston
Cool - will keep you in the loop as to the mechanics of that. Need to find fifteen minutes to think the best approach through.
- Cameron Neylon
hey neil, looks good
- Duncan Hull
Cheers, Duncan. Are you one of the cool kids with a Wave account? If so, does it work?!?
- Neil Swainston
Hi all those who liked. Did anyone try it in a Wave? Does it work? Thanks in advance for any help / feedback.
- Neil Swainston
Arrggh. Sorry, yes we tried and it seems to be broken. This probably just requires a few cycles of deploy and test but I'm not really in a position to do that this week. Maybe next week?
- Cameron Neylon
Thanks, Cameron. I'll keep prodding semi-interested parties. Can I also please reiterate my plea for an invite if any are lying around - the deploy and test cycles should be reduced if I can do the testing myself! Thanks.
- Neil Swainston
Neil, I have invites. If you have a GMail address, DM it to me, or else I'll use your Manchester one.
- Neil Saunders
Did we get Neil Swainston in in the end?
- Cameron Neylon
Neil Saunders has put me down for one. Just waiting for Mr Google to put it in the envelope and post it.
- Neil Swainston
Cool, good to know. We'll see you on the inside then
- Cameron Neylon
from twhirl
*pokes google*
- OpenSci Info
from IM
Thanks to Neil. I've got my account, and - would you believe it - the robot was kaputt. Amongst other things, Waves and Applets are not immediately happy bed-fellows... As I expected, I guess. Hmm...
- Neil Swainston
Neil, we can probably make some time to do some trouble shooting and testing in Wave this week perhaps? There are lots of little gotchas that are reasonably easily fixed.
- Cameron Neylon
Thanks Cameron. That would be very much appreciated. I made a fair bit of progress yesterday - it's a case of sticking applets within Gadgets. It now pretty much works. However, the applets periodically, and mysteriously, disappear. Any debugging tips from anyone?!?
- Neil Swainston
Winner of "Most Difficult Research Project To Justify To Grandma" contest 2009: Analysis of cricket ejaculate protein - http://www.plosone.org/article...
il tanz, Lucas Brouwers and Heather liked this
"Spermatophores were collected from males non-destructively, thus allowing multiple spermatophores to be collected from individual males throughout their reproductive lives."
- Noah Gray
from Bookmarklet
I'm assuming that "cricket ejaculate" is nothing to do with the nonsense that periodically spouts from Ricky Ponting's mouth?
- Neil Swainston
I am trying to make a list of wave robots and gadgets that I have tried.
Please feel free to add list of robots and gadgets (or links) that you have tried, tested or heard with a one line description.
Paul Bacchus, Carl Fulp, Laura Norvig and 12 other people liked this
Gadgets: Add equation - to add equations to a wave Map Gadget : to embedd a map in to a wave Yes/No/May be Gadget - to add a quick poll to a wave
- Khader Shameer
Robots: calcbot@appspot.com - Do some easy calculations inside a wave bitly-bot@appspot.com - Add bit.ly functionality to a wave emoticonbot@appspot.com - Add emotions to your wave easypublic@appspot.com - makes the wave public tweety-wave@appspot.com - tweet from wave wavehangman@appspot.com - self-explanatory :) embeddy@appspot.com - generates HTML to embed the wave on any page (useful for getting the (globally unique) Wave ID as well) elizarobot@appspot.com - a chat bot
- Khader Shameer
Thanks to @sparkymat for sharing his list of Robots.
- Khader Shameer
helpmeigor@appspot.com reference management, janey-robot@appspot.com interface to journal name author disambiguation service. Though off topic, we are arranging a science wave hackday in london (http://blogs.nature.com/wp...), search for waves with the tag "swlhd" and you'll find us. The source for both of these is available, http://github.com/IanMulv... and http://code.google.com/p...
- Ian Mulvany
are the source codes available for any of these robots? thanks for sharing the list!
- Mike Chelen
http://techpp.com/2009... - ultimate list of Google wave robots and gadgets
- Khader Shameer
http://sites.google.com/site... - The official Google Wave extension list
- Khader Shameer
Hi Mike. My first stab source code can be found here... http://mcisb.svn.sourceforge.net/viewvc... Source code is also available for the emoticonbot somewhere, too.
- Neil Swainston
Neil, cool thanks!
- Mike Chelen
Here goes blast, synthetic biology and other science robots http://www.abhishek-tiwari.com/2009...
- Abhishek Tiwari
synbiowave looks fun, and it is on sourceforge http://sourceforge.net/project...
- Mike Chelen
Khader, thanks for starting this list. I have been compiling bots and gadgets here: http://j.mp/gw-bots as well, I think the only one not on this this is sweepy-wave@appspot.com that removes empty blip waves. I hope everyone feel free to contribute to the site I started, because like this list, it is meant to grow and serve as a resource for the wave community.
- Justin H. Johnson
Justin, thanks for sharing the details about the resource.
- Khader Shameer
Could we have a list of google wave names somewhere so that I can figure out what Life-Scientists are on there?
Tom Tullius, Jeannette Høvring, Daniel Jurczak and 21 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 - seems to use the google contacts system like gmail
- Mike Chelen
pengwen.not.penguin@googlewave.com
- Parvez Halim
mstalnos@googlewave.com
- Tresterling
I'm on (thanks to Steve Koch!): tom.tullius@googlewave.com
- Tom Tullius
Considering design of an open-source spectrophotometer for under $100. Any ideas on how to tell whether led light output is enough for a given photodiode? And anyone know of any efforts in this general direction?
Anders Norgaard, Björn Brembs, Claudia Koltzenburg and 4 other people liked this
I have found this article, seems to be interesting, although a very simple setup: http://www.rsc.org/Educati... [edit: typo]
- Marcos de Carvalho
Another one: http://openwetware.org/wiki...
- Marcos de Carvalho
good line of thinking, we already have open source 3D printers why don't we have really basic & ultracheap open source (hardware/software) lab tools?
- Attila Csordas
Seems much in line with DIY Bio. Here's one example of a DIY sterile hood from Mackenzie Cowell's friendfeed: http://friendfeed.com/macowel...
- Steve Koch
@Attila, we also have DIY microarrayers: http://cmgm.stanford.edu/pbrown...
- Marcos de Carvalho
Also, my advisor has built an micro-injection device to produce transgenic Drosophilas, has worked pretty well. Here is the paper: http://www.scielo.br/scielo...
- Marcos de Carvalho
I don't think you will be able to make one for under $100 since the grating alone will break your budget. You may be able to find them on eBay but, you are risking getting a scratched grating. If you go the route of a prism, then you still have to deal with mounting it and getting a reasonable rotation mount (you still have to get this for the grating and it should be motorized so your...
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- Andy Maloney
I was thinkin of avoiding gratings altogether. I don't see why in principle you can't build something with a bunch of leds which have reasonable optical purity and a single photodiode. You would need to calibrate for each individual source diode but that's no great hardship - indeed it might actually help to provide an understanding of what an absorbance actually is. So manual calibration via 100% a 0% transmittance for each individual lights source like I used to do as an undergraduate :-)
- Cameron Neylon
Marcos - that RSC paper is very close to what I had in mind - thanks for the link - the OWW doesn't seem to have gone too far though...will have to track down Vincent and see how far it got...what i'm thinking of wouldn't be much use for actual spectral measurements but good for doing time courses or relative sample measurements - thinking around 10% accuracy and 1-5% precision over 0.05 - 1 AU
- Cameron Neylon
LEDs typically have pretty broad spectrums and can get fussy, such as peak wavelength shifts, if your power source isn't stable. There may be fewer problems with a broad band source and then using filters to pick off the wavelength you want. Of course, you could correct for wavelength shifts in the LEDs but that requires more optics. Hmm. Okay, I'm sufficiently challenged now to want to try and build something.
- Andy Maloney
How much of a shift? I've been looking at specs and most seem to be around 15 nm at FWHM which is no worse than what we use as the bandwidth on our plate reader when doing timecourses. Power stability is an issue though - although we'd probably be powering this off the USB from a computer - how stable are those in practice? My concern with filters is that they get pretty costly for...
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- Cameron Neylon
You're more than welcome to run off with any spectrophotometer data display / management stuff of mine... http://beaconw.cs.manchester.a...
- Neil Swainston
I think that I have come up with a design that might work. I'm not sure if it will, but it sure will be fun trying. I will make a special spot in my notebook for the design and build, and I will link to it once I get the parts in.
- Andy Maloney
from iPhone
Does XML *really* threaten big data? A rebuttal from Kurt Cagle http://xmltoday.org/content... @xmlsummerschool #xml #w3c
Michael Kuhn, Pierre Lindenbaum and Neil Saunders liked this
"If you're storing your XML data in a relational database repository, then you're throwing valuable money away, because you're adding a hideous performance penalty on every transaction."
- Duncan Hull
I keep saying this to the http://www.biomodels.net and SBML people but they seem to prefer relational databases...
- Duncan Hull
I consider myself an SBML person and I don't...
- Neil Swainston
there is nothing wrong with storing the data contained in an XML document in a corresponding relational schema and exporting and importing via xml. However if your actually storing the XML document as an entry in the database and using a combination of SQL and Xpath to query it - or worse only, ever returning the whole document, then that is questionable, and you should have some justification of performance against an XML-database.
- Frank
Is there a best practice for microbial genome annotation?
Rob Syme, Mike Chelen, Pierre Lindenbaum and 6 other people liked this
Nope. There are a variety of pipelines that perform similar tasks. Good starting point might be IMG documentation - http://img.jgi.doe.gov/w....
- Neil Saunders
Worth remembering that there is very little "best practice" in any bioinformatics. For a long time, we made it up as we went along. It's only this new generation of bioinformaticians that have any formal software engineering education and bandy around fancy terms like "best practice" to make us feel bad ;-)
- Neil Saunders
I think its more like the Perl culture "There is more than one way to do it !!" Best practices in bioinformatics is currently in an ad-hoc state of practice.Just like Damian Conways's Perl Best Practices is one of the best guide for good coding practices for Perl - hope we will also have a book on "Best Practices in Bioinformatics" soon, may be by a group of authors from LifeScientists room - what say ?
- Khader Shameer
@Khader thats why we need flexible guidelines and not the constrained best practice. Several minimal guidelines have been already worked out for the different aspects of the life science domain. MIBBI (http://www.mibbi.org/index...) can be a good starting point in this case.
- Abhishek Tiwari
I think very often in bioinformatics, TIMTOWTDI. It's not like software development, with a "task" and an "optimal solution". What I think matters most is that however you do it, it's documented and repeatable.
- Neil Saunders
I completely agree with you Neil, but some efforts towards developing well defined, documented workflows / protocols (can we call this as "Best Practices") to perform generic tasks (eg. annotation) will be useful for the community. I think several 'standards' (eg. MIRIAM/MIBBI) are developed to bring in a common frame work for routine tasks. I believe TLS is an ideal place to get a consensus about such practices and work on a wikibook of best practices in bioinformatics.
- Khader Shameer
And I agree with you. I'm all for standards and best practice. I'm also a realist and a practical bioinformatician :-)
- Neil Saunders
@Abishek : Best practices are not always "constrained", and constrained practices are impossible due to complexity of biological system - flexibility should be there. But my point is that even if MIBBI / other standards (http://www.mibbi.org/index...) are available for a long time - I've never seen them in research papers - is it due to poor visibility of such projects or no interest in promoting such initiative ?
- Khader Shameer
Khader, that's a good question. There seems to be a disconnect between standards developers and the people who should be using the standards. I think it's a publishing problem. Developers publish in computational journals and use computational jargon; users don't read those journals or understand the jargon.
- Neil Saunders
Khader, In my opinion the main motive of guidelines is to avoid the disagreement while best practices try to bring an agreement in community. Also, people are using these guidelines. Its just lack of awareness otherwise more and more people will adopt them. Take any Biomodels database model or CellML repository model, they are well annotated according to MIRIAM guidelines. Allyson...
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- Abhishek Tiwari
I find the line "it's not like software development" to pretty much sum up some of the problems in bioinformatics. Why isn't it?!?
- Neil Swainston
It's complicated :-) In part, it's because researchers are more interested in quick answers (= quick fixes) than good code. In part because it's only in recent times that bioinformaticians receive formal software training. In part, because biological problems are more complex than input -> process -> output and you don't always know exactly what you want to achieve when you start. And I guess, biological information has a lot of "context", not easily captured by simple routines.
- Neil Saunders
Hi Neil. Yep, all that you say is true. Just from a personal perspective, I've found that being "disciplined" in writing code (making nice, clean, interfaces to modules, unit testing, documenting) means that in the middle-to-long-run, quick answers are easier to come by. By building up a reasonably reliable library of classes (I'm a Java-geek), sticking the bits of Lego together is...
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- Neil Swainston
Neil, I absolutely agree. It took me some time to get to the point of trying to "do things right" from the outset - libraries, documentation etc. and I'm glad I got there. I think a lot of the problems stem from how academic research is conducted. "Can you just give me a table by tomorrow?" "Sure, let me write a library." "No, I just want a table." Hack together perl script, deliver table, discard, move on. Rinse and repeat, until contract expires. Leave mess behind.
- Neil Saunders
Couldn't put it better myself! I guess I'm lucky in so far as that I do have the luxury of longer timescales... until my contract expires.
- Neil Swainston
Thanks Abishek for the pointers to application of different standards. My point is the goal of both best practices and standards are the same - getting a consensus to do repetitive experiments / workflows. But as Neil's are discussing - the choice of individual bioinformatics projects is mainly to get a good fix, rather than an excellent code base. But hope some degree of consensus can be obtained if people can follow standards as a first step.
- Khader Shameer
Science isn't set up to reward coding standards. Funding agencies reward quick biological results, not infrastructure and software development. I'd argue that for every 5 biological grants, the NIH should be funding one software/database/computational infrastructure grant. The amount of data is only getting bigger.
- Chris Miller
I'd agree with that, Chris. Career wise, it's pretty much immaterial whether I churn out a hack or something "good" and reusable. It's quite annoying. Grrrr!!
- Neil Swainston
@Michael / Neil : I am agreeing with "Science isn't set up to reward coding standards", but as a subject in the interface of science and technology - it is high time that bioinformatics should embrace the standards. For Michael's question I was trying to make a point that if there is a standard/best practice/generic protocol for microbial genome annotation - he could have just followed...
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- Khader Shameer
I think genome annotation is an excellent example of how bioinformatics is not like software development. You don't just run a program and annotate a genome. There are lots of biological features: protein-coding genes, non-protein coding genes, motifs - all with their own associated metadata, all with various, disparate tools written specifically for each type of feature. Annotation is...
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- Neil Saunders
too right Neil. is there a best practice for violin-making, vision quests, or coming-of-age experiences? ;)
- Ian Holmes
:-) Exactly. The end result is what matters.
- Neil Saunders
srsly tho -- there are plenty of papers describing microbial genome annotation. it's still an open research area, but there are commonalities (repeats, transposons, genes, typical errors, ...) so I guess the rough union of those vague concepts would constitute the current best practice. not exactly a recipe...
- Ian Holmes
:D best practice for violin-making, vision quests, or coming-of-age experiences :D - Neil, in the current era of bioinformatics with Webservices and Work-flows - having an SOP/BP is always help you to kick start the work in minimal time rather than going through all genome project paper for the flowcharts for annotations.
- Khader Shameer
@ Ian : OK, finally that's something that Michael/any one interested in annotation to get from this thread.
- Khader Shameer
Khader, what we're saying is that in this case, there isn't an SOP/BP, because it just isn't that kind of procedure. But there is, as Ian says, plenty of advice available. I guess, in terms that CS people might understand, it's not agile. You actually have to put some work into understanding what's going on and what you want to do.
- Neil Saunders
@Neil - ^(chicken|egg)? - It could and should be that kind of procedure though. All the advice in the world isn't going to help the people that actually *use* your annotations. The current 'system' for annotating anything is so mindlessly broken I'm surprised it works at all. Now all it needs is a catchy name. Blight of Bioinformatics maybe?
- Paul J. Davis
Thanks for the comments everyone. I'm going to read as many genome papers as possible and try and put what I read together.
- Michael Barton
Just remembered this article: http://www.nature.com/nbt... whic is a good look at current annotation practices. I also finally found http://www.ncbi.nlm.nih.gov/genomes... which describe's actual paramters that NCBI uses for gene prediction.
- Paul J. Davis
Neil Saunders, I agree a lot of advice is available and it is definitely helpful. For example, I was not aware of something like MIARE (thanks to Abishek), am now implementing in our RNAi screen. But I can't agree with you if you define bioinformatics projects as non-agile. From a simple BLAST based sequence analysis to large scale data analysis is following agile approach. Think of n...
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- Khader Shameer
Thanks Paul,for the links to the articles.
- Khader Shameer
Khader, your very use of the word "agile" sums up what this is all about. Clearly you are "new school" bioinformatics and appreciate software development. "Old school" bioinformatics would never even use the word :-) As I keep saying, I don't disagree with anyone here who calls for better practices, standards or "agility". Just be aware that there are still plenty of old-timers around for whom bioinformatics means "hack together something that works."
- Neil Saunders
Here's a paper that describes how microbes are annotated in Swiss-Prot: http://dx.doi.org/10...
- Eric Jain
Neil : Just loved the definition "hack together something that works" :)
- Khader Shameer
Dear lazyweb... does anyone know of some good introduction to random access XML file IO with indexing? Say I happen to have a CML file with 100000 molecules, and want to index them so to quickly get the 7890th? Let's generalize this that the file is not newline formated, so molecule 7890 is not the XML snippets on line 789000-789100.
Mike Chelen, Jason Winget and Duncan Hull liked this
Most SAX parsers should be able to do this pretty much in a flash.
- Fergus Gallagher
@Fergus: I am not aware I can random access with SAX... AFAIK, I'd still have to 'pass' all the content before that specific XML snippet...
- Egon Willighagen
Yes, but SAX will fly though a file that size, giving you the byte offset (from start of file) of start end end of each element of interest. Write these out to a text file (the "index"), then use "cut" to extract the snippet of interest. Of course, I don't know anything about your specific requirements so this may be b****x in your context. Another approach might be to use SAX to...
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- Fergus Gallagher
Mmmm... it's been a while since I parsed 2 GB file with SAX... but if you think average seek times are acceptable... what SAX lib are you using?
- Egon Willighagen
Is it not a job for XQuery?
- Neil Swainston
I guess I wasn't clear - you only SAX-process the file once to produce a list of (start,end) offsets. But I'm now thinking that my second solution (reformat) is easier as it works with any SAX lib (not all provide access to the current offset).
- Fergus Gallagher
@Egon Ditto what Neil said, how about a native XML database?
- Duncan Hull
Don't even think you need to go as far as that, Dunc. If you're a Java spod, you could try the following: http://www.xquery.com/tutoria.... Sure equivalents will exist for other languages. Seems a shame to re-invent wheels by implementing your own means of indexing an XML file.
- Neil Swainston
@Neil but I thought re-inventing the wheel was what bio and chem-informatics was all about? ;-)
- Duncan Hull
@Duncan, ha! nice
- Rajarshi Guha
@Duncan :)
- Egon Willighagen
@Neil interesting. Going to check that out now...
- Egon Willighagen
Another question is what type of indexing are you wanting? If its purely UID based, then Tokyo Cabinet. If you want more flexibility and you're willing to deal with a bit of a slow down on indexing, then SQLite.
- Paul J. Davis
@Eric the index is made once... the use case is a file with very many molecule, sort of like a file based database, mostly view only, though for the plain text we do have write-on-safe. The user is browsing this file file viewing some 2-4 molecules at the time, and scrolling down should take considerably less than a second...
- Egon Willighagen
@Paul so, the indexing is a simple list index... 1087th molecules in the file, is the 1087th in the shown molecular table (as shown in http://bit.ly/4DGRmp where one entry in the file is shown) ...
- Egon Willighagen
Need to be able to scroll in both directions (and skip records)? If this is meant to be used in a desktop application: Would users download the index, or build it themselves? If records can be edited: Still need to be able to update the rest of the data?
- Eric Jain
@Eric. yes, both directions and skip. The index would be build on the fly. Changed can be cached and the real save is done, which could be done by a simple SAX run over the file, and replace the changed bits.
- Egon Willighagen
for a possible solution in Python, check out http://ff.im/7fGFz
- Adriano
So it looks like you could either have users import the file into a local database (FS, XML or key-value) and let them dump the data into a new file later when required, or you could index the file on the fly when opening it and merge changes from memory when saving. This second approach seems more appropriate if the main purpose of the application is to edit CML files?
- Eric Jain
If you need to get byte offsets out of the parser, try Woodstox. Few parsers appear to support this (or they return character offsets instead).
- Eric Jain
Not sure how reformatting the file to have one record per line would help -- unless each line were padded to have the same number of bytes (ugh). To jump to a specific record, you want to seek() rather than stream through the entire file (line by line, or otherwise).
- Eric Jain
Opportunity for initial development in Wave? - OMII UK Call for proposals in data management (pdf) http://www.omii.ac.uk/attach...
Björn Brembs, Nicolas Bertrand, Ant Beck and 2 other people liked this
Sounds good for a start: "Typically, projects will be 6 - 12 months in length and involve up to 24 person months of effort. Funding will be made under EPSRC terms and conditions, i.e. 80% of total project cost under fEC. The closing date for this call is 14/8/09 with funding decisions being made by mid September and projects starting from October 2009. All projects must be completed by the end of November 2010."
- Daniel Mietchen
Also looking at it it can involve experienced people in overseas places. I was thinking perhaps brilliant programmers marooned in the south of France?
- Cameron Neylon
from twhirl
I take it this is entirely unrelated to the following call...? http://www.jisc.ac.uk/funding...
- Neil Swainston
How can you write or be involved in a project if you don't know the capabilities of the application? Or is it just for a select group of insiders?
- Paulo Nuin
Its a separate call to the JISC one. I'm not sure that this would fit with the OMII call either but it seemed like it might be worth a shot. Paulo, we're just starting to get some idea, and have had some good discussions with the Google team and others over the past week. I'm not in a position to give out accounts but will be trying to dig into the possibilities and problems and making...
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- Cameron Neylon
Could one tie that up with our blog3 project (if that gets funded, that is)?
- Björn Brembs
I don't see why not - would be good to have that as an example of user interest in fact...
- Cameron Neylon
I'd be on board (if you're happy to have me :) - are we any closer to a formal release date for wave yet do you know? (I'm planning next semester's courses). Also - will there be a way to migrate LaBlog to Wave?
- Anna Croft
I'm looking when I have time to think at what would be involved in migrating the functionality of LaBLog to Wave. Some of it is easy, some probably difficult. But could be done with a full time developer I think. Yes, I'd be afer you as a test site definitely. Release data as it stands is "by end of year" as I understand it
- Cameron Neylon
from twhirl
If blog3 is the successor to LaBlog (??) and we get funded, this problem should be solved.
- Björn Brembs
Bugger about end of year - my course will be over by then. But at least it will hopefully be in time for remote supervision for sabbatical.
- Anna Croft
Well if we go with the OMII proposal that could be funded with expectation of starting in October. But I can't get my hands on extra Wave accounts until they are in proper beta
- Cameron Neylon
I suspect blog3 and Wave are orthogonal really - but Wave could be a front end to blog 3 (or any other triple store - which is something else to explore). The UI functionality probably makes more sense to implement in Wave in any case as this is likely to be simpler and more flexible.
- Cameron Neylon
Bring on the beta already.
- Anna Croft
If they indeed open source everything, the question only will be how to best merge the functionalities to have a tool that serves scientists best. I personally don't care what this tool will be called in the end. blog3 surely provides way more scientifically valuable functionality than Wave, but conversely, Wave has a lot of functionality I wouldn't want to miss for using blog3, if that makes any sense.
- Björn Brembs
I am returning from SciFoo 2009 at the GooglePlex and met there with a number of chemists and biologists who use PubChem. Many are complaining about it as filling up with junk and becoming of less value as it is hard to find quality information. Does anybody have any judgments/experience of this..good or bad? Similarly, what about ChemSpider?
Bill Anderson and Duncan Hull liked this
Nice to meet you Chemspiderman...
- Duncan Hull
I have not used PubChem very much, but am interested in the idea of "junk". How does this come about and what's the nature of the junk? Errors in primary submission? Poor curation? Metadata with insufficient evidence?
- Neil Saunders
Ditto Duncan...sorry we didn't have more time. I will be in the UK fairly regularly so maybe we'll connect again for a little longer next time
- Antony Williams
Neil...there is NO curation that I am aware of. What's deposited is left as is. This blog post discussed the issues we all have when assembling Public Compound databases.and is not unique to PubChem: http://tinyurl.com/nepaho . The comments I heard were that there is so much stuff flowing in that it's lost focus. The initial concept was to house data from the National Screening Labs but...
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- Antony Williams
We Manchester people have been generating large-scale systems biology models over the last few years, which we annotate with unique db identifiers from public repositories. Initially, we had no real preference towards a given repository for metabolites. However, over time we have gravitated towards ChEBI for a few reasons. The ChEBI people are very responsive to update requests for...
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- Neil Swainston
Neil, I had a conversation about ChEBI at Scifoo and can agree with your comments that it is a highly curated database. It is one of the best out there for sure. When I have found errors they are fixed very quickly in the next update. PubChem is not resourced to have a curation team and with 34 million compounds now.....hmmmm
- Antony Williams
Yep, I'm guessing that there is a real noise problem with PubChem. We're in the business of mapping experimental data to models, which involves matching metabolites (and enzymes) by their "unique" identifiers. The problem keeps cropping up with metabolites that are essentially the same, but differ in precision of stereochemistry specified (glucose and D-glucose), but at least with ChEBI...
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- Neil Swainston
Application of XML database technology to biological pathway datasets. - http://www.citeulike.org/user...
Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference, Vol. 1 (2006), pp. 4217-4220. The study of biological systems has accumulated a significant amount of biological pathway data, which is evident through the continued growth in both the number of databases and amount of data available. The development of BioPAX standard leads to the increased availability of biological pathway datasets through the use of a special XML format, but the lack of standard storage mechanism makes the querying and aggregation of BioPAX compliant data challenging. To address this shortcoming, we have developed a storage mechanism leveraging the existing XML technologies: the XML database and XQuery. The goal of our project is to provide a generic and centralized store with efficient queries for the needs of biomedical research. A SOAP-based Web service and direct HTTP request methods...
- Allyson Lister
Hi Allyson. Did you find any more details on this?
- Neil Swainston
@Neil I've read the paper, but I haven't looked for updated versions, nor tried the software yet. Basically, I was just curious as to how BioPAX has been used since its inception. I use BioPAX in my rule-based mediation work with model annotation (http://themindwobbles.wordpress.com/2009...), which I'm currently extending.
- Allyson Lister
Do you have a link for this, Allyson? The link from the following page ain't doing it for me... http://ieeexplore.ieee.org/search.... Cheers!
- Neil Swainston
New Nature editorial: How to stop blogging - "Organizers have only two options for their meetings: open or closed." - http://www.nature.com/nature...
Alexey, 'Mummi' Thorisson, Lars Juhl Jensen and 14 other people liked this
Nice to see Nature weighing in on this. I think this is the key point: "Any meeting to which anyone can register is fair game for all available communications technologies — and any rules that cannot be policed will be ignored anyway."
- Joe Bonner
I disagree. It is easy to set up a filter to catch blogging at real time, (see the CSHL incident) so registrants can be made aware of a no-blog policy, and sanctions that will follow breaking that policy. Also, meetings are not necessarily "all closed" and "all open" -- GRC meetings for example select their attendees. IMHO: large meeting with press etc. have no expectation of privacy...
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- Iddo Friedberg
I think this is all becoming very over-stated and confused. As Iddo says if you want a closed meeting - just have one. If it's open, new technology makes no difference to whether information can flow beyond the meeting, other than speeding the process. I can make an annotated sketch of your poster with pencil and paper if I'm really intent on taking the data away. Or you could just give me an A4 copy :-) And if you're at an open meeting and paranoid about stealing and scooping - what are you doing there?
- Neil Saunders
"And if you're at an open meeting and paranoid about stealing and scooping - what are you doing there?" Exactly.
- Neil Swainston
Just had a similar conversation about phud theses -- you could technically always get them but really they were not listed and difficult to get copies of, so there was this sort of limbo let's-not-think-too-hard-about-this approach. Afaik very few meetings ever feature anything really new -- it's more 'what we were doing last year'. Any electronic restrictions seem entirely circumventable through the use of pencil and paper anyway..?
- Chris
from twhirl
@Neil Saunders - agreed!
- Allyson Lister
I lost track of what was being debated here. It seems that we are all in agreement RE: meetings should just be "Open or Closed". Which is what the editorial is saying. The real debate is whether they *should* be open or closed. And this will differ from field to field. An interesting caveat suggesting how openness (although theoretically a good thing) can lead to an easy infiltration of the wrong kind of influence is being made here: http://ff.im/50myz
- Noah Gray
There's also a conversation going on at FF Science Online room about this same editorial.http://ff.im/4Y5Ts I was just going to make Noah's point when his response came in while I was writing - seems to me that Iddo and Neil's comments are along same lines as what the editorial is saying.
- Maxine
Anyone share software...? http://neilswainston.blogspot.com/2009...
Deepak Singh, Simon Cockell, Neil Saunders and 6 other people liked this
Might get more synergy if it is on git?
- Jason Stajich
Left a comment... I think this is good news: 'they' now seem to agree that we are doing science, and that someone may steal our science.... Good, progress, good.
- Egon Willighagen
I'm not entirely sure what I'm doing *is* science. That's not to say that that rings true for all bioinformatics.
- Neil Swainston
Re: above comment - I think that facilitating science is at least as important as doing it.
- Neil Saunders
Ship-shape and Banksy Fashion - http://duncan.hull.name/2009...
Konrad Förstner and Allyson Lister liked this
Graffiti artist or blogger?
- Duncan Hull
He's not without his critics: http://news.bbc.co.uk/1...
- Neil Swainston
@Neil its those pesky graffiti "artists" getting their revenge
- Duncan Hull
Bioinformatics and Systems Biology: Multidisciplinary scientists versus Interdisciplinary scientist - http://www.abhishek-tiwari.com/2009...
Madhu Pandey, Mike Chelen and Allyson Lister liked this
Interesting question. After three years in a *inter*disciplinary biocentre, I'd hazard that the Great and the Good in the computer science building would burst out laughing if I wandered up to them and asked for a lectureship.
- Neil Swainston
Daily Mail-o-matic | qwghlm.co.uk - http://www.qwghlm.co.uk/toys...
Mr. Gunn, Jim Downing, Peter Miller and 10 other people liked this
A new Daily Mail headline every time you click the button. Now updated to include 2009 bogeymen! I was going to give the generator a sophisticated grammar for more varied sentences, until I realised the Mail’s grammar is nearly always the same. If you like this, you might also like the The (New) Daily Mail Oncological Ontology Project - tracking Daily Mail’s classification of inanimate objects into two types: those that cause cancer, and those that cure it.
- Duncan Hull
NICE ONE, Duncan. After 6 spin's my pers. fav was:- "WILL DUMBING-DOWN KILL CLIFF RICHARD?"
- Graham Steel
"HAS THE METRIC SYSTEM GIVEN HOMEOWNERS CANCER?" Scarily realistic, these.
- Matthew Todd
Brilliant. "Could Gordon Brown turn the countryside gay?" You be the judge.
- Neil Saunders
WILL TEACHERS GIVE BRITAIN'S FARMERS DIABETES?
- Duncan Hull
Double-plus like. Great Friday afternoon site.
- Frank Norman
HAS GORDON BROWN GIVEN CLIFF RICHARD SWINE FLU? (should have noticed this website to brighten up my mood when discussing unethical marketing...)
- Egon Willighagen
"Has the MMR jab impregnated your pension" ... lol
- Deepak Singh
"Is Jacqui Smith Burgling You?"...hang on...that's not really very funny is it...?
- Cameron Neylon
"WILL THE E.U. STEAL THE IDENTITY OF THE CHURCH?" yikes! thanks :)
- Allyson Lister
The Daily Mail Ontology project is pretty good too http://dailymailoncology.tumblr.com/ they've classified everything in the world into just two classes, things that cause cancer and things that don't :)
- Duncan Hull
Duncan... yes, excellent suggestion! We should RDF-ify that for the LODD effort! Try aspirin! A wealth of information! :)
- Egon Willighagen
Oh, and don't get tempted to install that GreaseMonkey script on your colleagues machines :)
- Egon Willighagen
The utterly absurd ones are my favourites. "WILL LESBIANS HAVE SEX WITH HOUSE PRICES?"
- Neil Swainston
YMCA: Just a little bit of GTCA! - http://duncan.hull.name/2009...
Neil Swainston liked this
I wonder how many squillionaires in the marketing department had to put in endless nightshifts to dream this up?
- Neil Swainston
@Neil some people have all the fun...
- Duncan Hull
German comedy ambassador Henning Wehn on the european sense of humour (youtube.com) - http://www.cs.man.ac.uk/~hulld...
Dave Munger and Neil Swainston liked this
Roll on Sunday. Ausgezeichnet!
- Neil Swainston
quote "British always say we Germans don't have a sense of humour. I don't find that funny." --Henning Wehn
- Duncan Hull
@Neil Ja!
- Duncan Hull
Informal Knowledge Sharing in Science via Social Networking - http://themindwobbles.wordpress.com/2009...
Neil Swainston, Jean-Claude Bradley, Jan Aerts and 3 other people liked this
This is a cross-posted item available both from this, my home blog, and http://biosharing.org, a new blog specifically concerned with “news and information about activities related to the development of data policies and standards in the biological domain, in particular for the area of ‘omics”. You can find the post on biosharing.org at: http://biosharing.org/2009... . Recently, [...]
- Allyson Lister
Liked the piece, Allyson. I can see the point regarding reporting from conferences and such-like (something you did with consummate professionalism in Cambridge, for example). Just looking the FriendFeed, though, I'm beginning to get the impression that 99% of users are, in the nicest possible way, informatics geeks like me. Why are my lab-based colleagues on Facebook and not on Twitter?
- Neil Swainston
Introduction to Ontologies in OWL @ Manchester - http://www.co-ode.org/events...
Amund Tveit, Björn Brembs, Abhishek Tiwari and Duncan Hull liked this
The University of Manchester Bio-Health Informatics Group and NIBHI invite you to participate in a their internationally renowned two-day tutorial on Ontology engineering and OWL. This two-day introductory ‘hands-on’ workshop aims to provide attendees with both the theoretical foundations and practical experience to begin building OWL ontologies using the latest version of the Protégé-OWL tools (Protege4). This tutorial will cover the main conceptual parts of OWL through the hands-on building of an ontology of pizzas and their ingredients. A series of exercises take attendees through the process of conceptualizing the toppings found on a pizza; the entry of this classification into the Protégé environment; the description of many types of pizza. All this is set in the context of using automatic reasoning to check the consistency of the growing ontology and to use the reasoner to make queries about pizzas. Since 2003 this tutorial, in various forms, has been given over 20 times and been attended by hundreds
- Frank
You almost had me there until I saw the price...actually I can't do the dates anyway but £200 seems a bit steep for two days.
- Cameron Neylon
@Cameron its worth the money, the tutorial is very good!
- Duncan Hull
And I guess it includes the pizza?
- Cameron Neylon
Ontological Pizza yes http://www.co-ode.org/ontolog... not sure about real pizza...
- Duncan Hull
I understand that it does indeed include real pizza. I was a the last one, but as I'm a local, I skipped the meal out at Croma http://www.croma.biz/manches.... Course wasn't bad, either...
- Neil Swainston
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