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Andreas Matern › Likes
I'd like to extract, for a rather long list of human genes, info on tissues or cell types where they are known to be important in some automated way from literature. Any suggestions for where to start? Extracting Gene Ontology terms will miss many known gene-tissue associations. Is there a text mining tool that can find gene/cell-type associations?
Andreas Matern, Carl Fulp, Nakao M. and 3 other people liked this
Only starting point that I can suggest is Acembly: see for instance http://www.ncbi.nlm.nih.gov/IEB... - then click "expression tissue" in menu bar at top of page. I don't know how easy it is to mine - there are some downloads available. NCBI GEO Profiles might be another entry point. There are sure to be tissue expression databases but I don't know what they are.
- Neil Saunders
Now I think some more, BioGPS (successor to SymAtlas) is also a good start: http://biogps.gnf.org
- Neil Saunders
Thanks Neil, AceView is a nice resource that I had forgotten about. I think I can get started by digging there. BioGPS I had already been playing around with. It is also a great resource, but I would like to collect literature mentions of genes in the context of tissue specific activity and/or diseases in addition to expression data.
- Mikael Huss
You may want to have a look at HPRD (Human Protein Reference Database) http://www.hprd.org/ . The database is reporting gene - tissue information based on extensive literature curation.
- Khader Shameer
Thanks, Khader, another good suggestion. BTW, http://www.proteinatlas.org/ is a nifty resource, but it does not seem to provide any kind of downloads.
- Mikael Huss
I'm not sure if there are Genetics/Celluar biology professionals on http://sciencestack.com yet, but you might want to try to ask there.
- Jane Breezler
now is the perfect time to read An introduction to scripting in Ruby for biologists by @jandot & Andy Law http://www.ncbi.nlm.nih.gov/pmc...
Andreas Matern, Ian Simpson and Endre Sebestyen liked this
Writing a parser in Javascript : Top Down Operator Precedence - http://javascript.crockford.com/tdop...
Andreas Matern, Tracy, Ian Holmes and Pierre Lindenbaum liked this
sweet!
- Ian Holmes
from BuddyFeed
Fwd: Scholarly Identity 2.0: Matrix, Concept Model, and Presentation - http://mchabib.com/2009... (via http://friendfeed.com/habib...) (Full description of how these models interact and an overview of the presentation.
Mickey Schafer, maxilprof and Andreas Matern liked this
US, UK, Australia and New Zealand now all have official national-level open data sites.
JoeCamel, Andreas Matern, Sarah Kendrew and 3 other people liked this
thank you, where exactly can these be accessed?
- Claudia Koltzenburg
http://data.gov/ , http://data.gov.uk/ (registered access only) , http://data.australia.gov.au/ , http://data.govt.nz/
- Richard Akerman
from BuddyFeed
The Ultimate Productivity Blog - http://productiveblog.tumblr.com/
Andreas Matern, Allyson Lister, Pierre Lindenbaum and 3 other people liked this
I was just thinking "that sounds like a time-waster", but they were one step ahead :-)
- Neil Saunders
Great, that really helped me!!!
- Konrad Förstner
Pee-wee Herman Makes His First Tweet on Twitter - http://laughingsquid.com/pee-wee...
Iván Abrego, Andreas Matern, sean808080 and 2 other people liked this
I want to easily annotate, share and compare gene sets with other group members. What is the best tool? I have looked at Gene Set Builder, WebGestalt and Genephony. Have not found exactly what I'm looking for. What do you use?
Richard Klancer, novoseek, Khader Shameer and 2 other people liked this
I have used something less sophisticated GeneVenn earlier, will try other tools you have suggested. Can you elaborate a bit on what you are looking for ? Also Fwd your query to The Life Scientists group.
- Khader Shameer
Our group wants a repository of interesting gene sets. With references, comments, tags, etc. Both our own gene sets, and published by others. All gene sets I upload should be automatically available to other group members. Don't need the advanced features of the tools I mentioned. A collaborative version of GeneVenn (thanks!) is what I'm looking for.
- Torfinn Nome
Have you looked at NextBio? I would be happy to answer any questions or show you what it can do. Lisa
- NextBio
Yeah, Lisa I was checking if such a feature is available with NextBio. If not, you guys can easily incorporate it - right ?
- Khader Shameer
We have share and compare tools. As far as adding new features - well, we can build new features pretty easily and we can even build them quickly, but there is a looong list of new features already in the queue and a new feature you request might not get released quickly. We do have APIs.
- NextBio
I think API's are available only with NextBio professional license. No donuts for me :( !
- Khader Shameer
Early Risers Crash Faster Than People Who Stay Up Late: Scientific American - http://www.scientificamerican.com/article...
Brian Krueger - LabSpaces, Andreas Matern, Ruchira S. Datta and 14 other people liked this
"An hour and a half after waking, early birds and night owls were equally alert and showed no difference in attention-related brain activity. But after being awake for 10 and a half hours, night owls had grown more alert, performing better on a reaction-time task requiring sustained attention and showing increased activity in brain areas linked to attention. More important, these regions included the suprachiasmatic area, which is home to the body’s circadian clock. This area sends signals to boost alertness as the pressure to sleep mounts. Unlike night owls, early risers didn’t get this late-day lift."
- Donnie Berkholz
from Bookmarklet
I knew it!
- Fossil Huntress
I always secretly knew we night owls were better adapted than those crazy-up-before-dawn people!
- Her Lindsay-ness
Posted at 11:15 pm local time ... and still going strong!
- Donnie Berkholz
is SA late to this - that paper came out a few months ago. There was some good coverage of it, e.g., http://sciencenow.sciencemag.org/cgi...
- Bora Zivkovic
Slow and steady wins the race :-)
- Neil Saunders
For the record, I'm liking this at 12:32 AM Eastern.
- Chris Lasher
This reminds me, it's 5:58am here... Off to bed.
- Ricardo Vidal
from iPod
darn, now i have even less motivation to switch to an early-bird schedule
- Wladimir Labeikovsky
Glad to see one positive about us night owls. Many are touting the harm of going against circadian cycle. Have been a day sleeper for ten plus years-no harm no foul.
- Celt MacGann
I know this feeling... Have had far too many days where my brain only really starts to wake up at 6pm, just in time to leave office because girlfriend/social life/other commitments are calling
- Andrew Clegg
This is the most visited post on all of my blogs at all times: Everything You Always Wanted To Know About Sleep (But Were Too Afraid To Ask): http://scienceblogs.com/clock... Four years old but still pretty much up to date. Explains it all.
- Bora Zivkovic
BUT...us early birds get a whole day's work done in that first hour and a half...lol
- Mary Canady
@Bora spectacular post! Love the wealth of information and dearth of politics :) Feel less guilty and more hopeful already. Here's one of my favorite lines from Bora's post: 'Of course, all of the above are the strategies to shift your clock to a "socially accepted" phase. But you are not crazy or sick. It is the societal pressure to get up at a certain time that is making you sick. Try...
more...
- Steve Koch
@ Bora -- loved the post, too! I especially appreciated the discussion of light -- I spent a few months reading up on the impact of light, and a Science channel feature on biochronology a few months ago found that very bright light did a lot to help Alzheimer's patients and that planning around an individual's circadian rhythm could ease the side effects of chemo while increasing...
more...
- Mickey Schafer
That was my first true science post, from January 2005, the one that showed me there is interest in this and I could move from blogging politics to blogging science. I posted it on a brand new blog that nobody knew about, just set up, and the next day it was linked by BoingBoing, Andrew Sullivan and others. Even today, it is still my most visited post ever (and that counts ONLY the...
more...
- Bora Zivkovic
The web as platform: Search as UI - http://mndoci.com/2009...
Andreas Matern, Andrew Perry, Neil Saunders and 2 other people liked this
Another example that comes to mind is using InChi for describing small molecules - as far as I remember the InChi representation was explicitly designed to be search engine friendly (unlike the already established SMILES representation).
- Andrew Perry
Differential expression analysis with Bioconductor and Python - http://bcbio.wordpress.com/2009...
Andreas Matern, Neil Saunders, Andrew Perry and Rajarshi Guha liked this
popsicle stick of impending doom
Rick Cogley, Christina Kuhn, Lu Tao and 72 other people liked this
:o
- chaz2b
OMG!! This just made the night for me! LOL Mind if I re-share?
- Carlton Hackett
o_O
- Alix Whitmire
what's this ?
- 鸿蒙
well that would have been a shock eh lol
- eric
fucking hell
- i ♥ derrick #bellymeme
Get more icecream!
- Jacob
"I've seen things you people wouldn't believe. Attack ships on fire off the shoulder of Orion. I watched C-beams glitter in the darkness at Tannhauser Gate. All those moments will be lost in time, like tears in rain…. Time to die."
- Jim Norris
I don't like it when food threatens me. Or the invisible iguana under my bed. He's a real bastard.
- Roger Benningfield
HELP! I'm trapped in a popsicle stick factory.
- DGentry
I've seen this movie, and Bruce Willis is standing behind you with a lethal bombpop.
- Peggy Gartin
Peggy, that is hilarious!
- Jacob
HEE!
- Felicia Yue
Drugs in Portugal: Did Decriminalization Work? http://www.time.com/time...
Jonathan Speigner, Urbansheep, ǝuǝƃnǝ and 6 other people liked this
"Portugal, which in 2001 became the first European country to officially abolish all criminal penalties for personal possession of drugs, including marijuana, cocaine, heroin and methamphetamine."
- Joel Webber
"At the recommendation of a national commission charged with addressing Portugal's drug problem, jail time was replaced with the offer of therapy."
- Joel Webber
Wow, I did not know this, and it's great.
- Tudor Bosman
"Judging by every metric, decriminalization in Portugal has been a resounding success," says Glenn Greenwald, an attorney, author and fluent Portuguese speaker, who conducted the research. "It has enabled the Portuguese government to manage and control the drug problem far better than virtually every other Western country does." - other countries take note.
- Brian Sullivan
There's a bit at the end where a naysayer says something to the effect of ~"this only proves that drug use failed to *increase* under these policies". I read the report differently, but either way it takes some of the wind out of the sails of the "legalized drug use will turn us all into junkies" camp.
- Joel Webber
Meant to say this earlier: Vamos na Portugal!
- Joel Webber
NCBI Genome Workbench Home Page - http://www.ncbi.nlm.nih.gov/project...
Bill Hooker, Marcos de Carvalho, Berci Mesko, MD and 5 other people liked this
Genome Workbench can display sequence data in many ways, including graphical sequence views, various alignment views, phylogenetic tree views, and tabular views of data. It can also align your private data to data in public databases, display your data in the context of public data, and retrieve BLAST results. Genome Workbench is built on the NCBI C++ ToolKit and uses cross-platform APIs for graphics. It runs on your local machine, and is available for Windows 2000/XP, Linux, MacOS X, and various flavors of Unix. Download recent versions from the NCBI Genome Workbench FTP Site , or choose one of the download links below:
- Pierre Lindenbaum
Tried to build this years ago and failed. We've both improved since then, should give it another go.
- Neil Saunders
That's interesting, anyone using it yet with their own data?
- Andreas Matern
Human landscapes from above - The Big Picture - http://www.boston.com/bigpict...
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Darren Heydon, Bertrand Doux, Jonathan and 37 other people liked this
amazing. Makes me want to go out and buy an airplane.
- Thomas Hawk
I wonder how far out in advance they have to arrange to take those pictures. All by one photographer from across the globe...
- Kevin Kuphal
I just love this kind of photography! Beautiful.
- Rachel Lea Fox
I guess you all know Yann Arthus Bertrand's "La Terre vue du ciel": http://bitly.com/B0gGl. He's also behind Youtube "Home" project: http://www.youtube.com/user....
- Jérôme Flipo
luv those pictures, one of best series seen! great job ;)
- Dani Martínez
I love the picture of the Maunsell Sea Forts. Looks like it would be fun to visit.
- Ross Miller
I'm thinking about putting a proposal to bring our data resources kicking and screaming into the Semantic Web. I'm thinking RDF publishing, Linked Data compliance, microformats, ontological tagging. Has anyone been involved in a project like this? Anyone care to share experiences or ideas?
Dave Bridges, Luis Enrique León, Peter Ansell and 29 other people liked this
No huge amounts of experience but starting down that same road as and when we can so would very much like to share the experience and ideas
- Cameron Neylon
What do you mean with "our data resources" ? :-)
- Pierre Lindenbaum
I work in Christine Orengo's lab at UCL, so primarily CATH and Gene3D, any parts of our internal data warehouse BioMap that might be useful to others, and spin-off projects from these. http://cathdb.info/
- Andrew Clegg
First things that come to my mind; describe your projects using the DOAP ontology, your staff using FOAF, create an ontology for your data (e.g. see Eric Jain's work (http://friendfeed.com/ejain) on uniprot)( see the NCBO for not re-inventing the wheel), add RDFa to your web pages, make your data available as RDF , etc...
- Pierre Lindenbaum
I like the idea of RDFa as a good way to start sneaking semantic markup in without major upheaval, thanks Pierre. DOAP for biological data resources -- interesting -- could maybe do with extending a little
- Andrew Clegg
It's still unclear to me what the value of this is today, to the people doing it or anyone else ... could anyone help me out?
- Donnie Berkholz
We just put in a proposal to build our data repository, and then publish our data. I would be interested too in hearing others experience. FYI, the Bio2RDF site has some info on how they rdfized their data - http://bio2rdf.wiki.sourceforge.net/Namespa...
- Melanie
@Donnie that is a fair point and one often mentioned. Fine if you are starting from scratch like Melanie, but if you already have you data in an RDMS, what is it that this RDM system is not providing that RDF could? Anyone....?
- Frank
@Frank easy integration via common protocol (sparql) with other resources? If I want to access your data I don't need to know about your webservices, or parse your files for example. If I query your database and get a result, I can directly pass it on to the next resource, no need to input it to an other script or website.
- Melanie
@Melanie are you not making the assumption the "other" resource is in RDF? RDBMS have a common protocol, SQL.
- Frank
@Frank - Indeed, the point being that it is easier with RDF. My repository is planned as an Oracle RDBMS, and I am looking into rdfizing my resource, or translating at query time. Some template queries are available at http://sparql.neurocommons.org/. Doing the same querying individual databases would be much more painful.
- Melanie
@Donnie something like DOAP allows robots to find your data (and their meaning)
- Pierre Lindenbaum
Pierre has an excellent set of suggestions, and let me add one more: Write a detailed account of what you did and problems you faced along the way to make it easier for the next guy to go down that road.
- Mr. Gunn
@Frank: If you think SQL is a "common protocol", then you haven't been using more than one RDBMS :-)
- Eric Jain
Liked cause this is a fascinating discussion
- Deepak Singh
@Gunn yep, that'll be the paper at the end :-) @Frank and Donnie -- you wouldn't want to give Johnny Random access to your RDBMS remotely would you? Even read-only, the ability to run arbitrary queries could bring it to its knees. But with RDF, the raw data is there at a sufficient level of granularity that they can run arbitrary and unlimited queries at their expense across all your data...
- Andrew Clegg
... not to mention, mashups of your data with other people's. Plus, I like where this is going and how quickly it's growing: http://www4.wiwiss.fu-berlin.de/bizer... ... and I don't want to continue not being on it
- Andrew Clegg
@Mr Gunn : I started to think about how to RDF-ing my data. I'm currently stopped, because I would like to handle those data with some mysterious tools (Taverna, Biomoby, semantic-ws, etc... ) but I still haven't understand how to use them.while I'm sure there is something good to do with them.
- Pierre Lindenbaum
@Andrew Ensembl, UCSC and GO allow an anonymous access to their mysql DB. e.g. mysql -N --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg18
- Pierre Lindenbaum
Is that entirely sensible? As an occasional DBA and SQL developer I'm well aware that a badly-written query on a large join can be indistinguishable from a DoS attack
- Andrew Clegg
Some databases (e.g. Oracle) have detailed options to restrict the resources that can be used per user or query. For databases that use one-process-per-query (e.g. PostgreSQL) you may be able to use OS-level process limits. I'd be interested to hear how Ensembl handles this!
- Eric Jain
you can limit the resources of an account http://dev.mysql.com/doc...
- Pierre Lindenbaum
It would still make me nervous. I've worked at organisations where even internal people outside the DW team aren't allowed to execute arbitrary queries. However I've just derailed my own thread so what do I know :-)
- Andrew Clegg
In the case of UCSC I think they have a dedicated and isolated mysql server where the data is copied for this external use.
- Pierre Lindenbaum
Just so we're not comparing apples to oranges: Direct access to a RDBMS via SQL is comparable to direct access to an RDF database via SPARQL. The data we can get this way (i.e. tab-delimited or RDF data, resp) could be obtained through other channels (e.g. FTP, which is less flexible, but more suitable for large amounts of data).
- Eric Jain
I kinda wish I hadn't mentioned query cost as an argument against direct SQL queries. That's actually a side issue. The most important part of RDF publishing seems to me to be the ability to mash up one source of data with another (and another and...) -- breaking down those silo walls and following chains of knowledge across the web
- Andrew Clegg
That's why we're all looking for a stable common identifier for our data (remember LSID http://en.wikipedia.org/wiki... ?) and that's why you should use an already existing ontology ( http://bioportal.bioontology.org/ ) rather than creating your own vocabulary.
- Pierre Lindenbaum
That might be the main argument: SQL (and tab-delimited data, and XML) have no (standard) way to express that some column/value isn't just a string, but represents some concept in another database (which we may even be able to retrieve if we need it and don't have it locally).
- Eric Jain
I'm all about the not-reinventing-the-wheel Pierre
- Andrew Clegg
If we were able to agree on one central, specialized identifier system and all use the same, non-overlapping vocabularies, RDF might be overkill. Until then, it seems rather useful to have a system that allows us to disambiguate and map our different wheels to each other (and disagree over what ought to be mapped to what).
- Eric Jain
One project mentioned on another thread is Okkam(http://www.okkam.org), an EC/FP7 funded project to build infrastructure for an entity naming system. Dunno about others, but personally I find it a bit weird that it has such a low profile online, being a big (?) project. Anybody know more about this?
- 'Mummi' Thorisson
"The key objective of the [Okkam] project is to deploy a global and open service called Entity Name System (ENS), which will support the systematic reuse of identifiers for "things" on the Web and generally on the Internet"
- 'Mummi' Thorisson
Someone from Elsevier mentioned Okkam in a talk at SESL. I couldn't help thinking that the goal of giving every 'entity' on the web a UID was a bit, well, unachievable. Still, aim high I suppose
- Andrew Clegg
To pass on a comment from a mate (who looked into Okkam some more), regarding their low profile: " Since the project is due next year, there's not much time left to involve the community... Amazingly they do offer plenty of tools, like the Word and Protege plugin."
- 'Mummi' Thorisson
How did they call the community ? I didn't find any ref on pubmed ....
- Pierre Lindenbaum
@Pierre: Their community involvement strategy is all layed out in this password protected document: http://www.okkam.org/deliver... :-)
- Eric Jain
Their website isn't very communicative, but here is a paper that explains the project: http://events.linkeddata.org/ldow200.... Still doesn't make much sense to me though...
- Eric Jain
The Shared Names - http://sharedname.org/ - project is worth mentioning too. They are meeting next week (http://sharedname.org/page...)
- Melanie
With all those competing projects for centralizing identifiers, you'd think that people would have realized by now how futile this approach is...
- Eric Jain
@Eric, yes, I was playing devil's advocate in these sense with regards to SQL protocol, well of course putting all you data in the same format will give you a single protocol. Which I thinks is the same thing you said in your "apples and organges" comment. I am not sure that answers the question, why RDF?
- Frank
So just to clarify, I am all for publishing data as RDF, linkedata etc and this is something I am trying to raise the profile of where I am working now. However, the standard response so far has been, " We have our data in SQL and we can do what we want to do, when people ask for some information we give them a spreadsheet of it". @Eric, I would be interested to know if anything like this occurred in Uniprot and how you counteracted it. We have FASTA. TEXT, XML, why do we need another format in RDF?
- Frank
Sumarising so far, I should use RDF becasue I get: 1)integration with other RDF resources with a common protocol 2) Dont need to understand the datastructure/schema, therfore no file parsing - (bioinformaticians out of jobs :) ) 3) Similar to 2, but the direct output of a query can be the direct input/integrated with outher resources without the need for parsing 4) Access to data,...
more...
- Frank
6) Extra value (similar to 1) to data can be added via mash-ups with other resources - either by the provider or external parties. The provider has the potential to gain extra value without putting effort in to do so 7) Ontolgy annotation, the ability and a standard way to add meaning to data that is computationaly ameneable, which is harder to achieve via SQL
- Frank
Plus, you can annotate web services with the semantic types they accept and produce (see SAWSDL) so you know any data published with a conforming type will fit. Not sure how many people are actually doing this yet (we're not). But you certainly can't do that sort of thing with direct DB access or table dumps
- Andrew Clegg
fantastic discussion :) Might be suitable to also include a link to the article about the 10th anniversary of RDF, as linked on FF by Frank, Abhishek, Yann, Pierre, etc: http://friendfeed.com/e...
- Allyson Lister
Yeah, I just downloaded that one, looks like a good intro
- Andrew Clegg
FASTA is perfect for people who just need the sequence data (including an identifier and a human-readable label). But it's not advisable to put much more than that in there (some have tried)...
- Eric Jain
TAB-delimited data is great for "flat" data such as lists of identifiers. But it won't work well for complex data (data types, references) without a RDBMS-specific schema. Also, once the data has to be split into multiple files, it's no longer practical to process the data without loading it into an RDBMS first.
- Eric Jain
TEXT has a lot going for it: It's by far the cheapest solution to work with as it can be edited and displayed directly. But it gets quite ugly as the data gets more structured (natural for a growing database) and code needs to manipulate the structure in more detail rather than just passing around blobs of text.
- Eric Jain
XML can get rid of the custom syntax quirks that tend to accumulate in text formats. But we now need to invest quite a lot of effort into creating human-readable/editable views of the data, and shuffling around the data (especially large amounts) is a lot more involved. There are some code generation tools, and to pass around complex data without handling it there is a generic tree data model. XQuery can be used to query within (sets of) documents.
- Eric Jain
RDF addresses some of the issues XML leaves open (e.g. how to identify and reference resources globally) and provides a much more useful (for data integration, at least) non-document centric, graph-based data model (plus a standard query language). The "schema" language (OWL) is more focused on describing logical constraints than syntax (as is the case with XSD).
- Eric Jain
Note that all of these formats can either be generated on the server-side based on some (more or less standard) query mechanism, or they can be pre-generated and distributed in bulk (e.g. via FTP). So that's really a separate issue. For publishing data, I consider TEXT and XML to be legacy formats (i.e. you might need to continue to support them, but wouldn't bother providing them for new databases).
- Eric Jain
@Eric have you any indication that anybody is using RDF_uniprot and what for? Or if anybody else for that matter knows how its being used.
- Frank
The RDF distribution of UniProt was being used in various RDF demonstration projects. Don't know if anyone (outside of UniProt) has started using it (the main part, not just the smaller parts such as the taxonomy) for "real" work since then (i.e. end of 2007).
- Eric Jain
short film featuring inanimate objects from the streets of NYC animated using the voices of interviews with New Yorkers http://laughingsquid.com/the-los...
Jason Stajich, Robert Kenney and Andreas Matern liked this
Have you installed the FriendFeed notifier yet? https://friendfeed.com/account...
Otto, HealingBrush, Kyle Weller and 88 other people liked this
The notifier is my favorite new feature in a long time. Try it out and let me know what you think. (it works on OSX, Windows, and Linux, btw)
- Paul Buchheit
Yes, it is pretty darn great, especially when you have it focus on a short list of people you really must interact with in almost realtime. With it turned on to too many people, it is an overlapping chore. Thanks for the cool apps!
- Josh Haley
I try it ones, but no. Somehow I have come to dislike notifiers... Not my thing, I ratherly use sidebar on firefox :)
- Kristian Salonen
I just did. Thanks for the reminder!
- Robert Scoble
So Did I!
- Helen Sventitsky
Wow, this is slick. Turning off gtalk now
- Christian Burns
Yes, and <3... wish it was resizeable, though. excellent otherwise.
- .LAG liked that
Nope. Adobe Air sucks huge resources. My Mac only has 4G of RAM and I can't run Air Apps.
- Glen Campbell
I love it. It's the least intrusive Air App I've seen. I would like the ability to add my comments and likes and a list. That would really make it easier to keep up with conversations. :)
- Andrew
LOL@4G RAM. My main laptop has 512MB
- Rahsheen ™, Coach of FF
Glen, Air can be a resource hog, but the notifier seems to use less memory that some other Air apps (on my computer, TweetDeck has a 283MB resident size, by the notifier is only 54MB).
- Paul Buchheit
air... ick... installed, but not too hopeful
- anna sauce
man, i'm wishing i hadn't downloaded. i already have growl notifications and mail notifications ... overwhelmed.
- Lynne d Johnson
You can have FF and Twitter on your desktop with one app: Thwirl. And, with Thwirl you can turn off ALL notifications.
- Phil Essing
from twhirl
Yes, but only works sometimes and when it works, it's updates popups hell. :)
- Rui Pereira
@JoshHaley I agree, great for a small subset like coworkers or family, but not for your entire feed.
- karl dotter
Ok, a couple thoughts. Once I installed the app I had updates constantly, often one over another so this means #1) I am missing way too much good content, #2) I have a very rich experience on Friendfeed since I seem to want to ignore most Twitter updates but want to click into most FF updates, and #3) if I left this thing on I would get zero work done. This application is too dangerous for me. Sorry guys, i had to turn it off. Good to see you are making the experience flexible for all though. Thanks.
- Eric @ CS Techcast
Oh and +1 for using Morton's Duran Duran post for the app!
- Eric @ CS Techcast
The problem I have with AIR is that it wakes up the CPU constantly. air apps + battery life = fail.
- mjc
Phil, Thwirl is a full desktop client, which is great if that's what you're looking for. The notifier is just a very simple and lightweight notifier, which makes it very easy to passively keep up with what's happening on FriendFeed in real-time.
- Paul Buchheit
I liked Eliza more :p
- Rodfather
wish you could disabled comments...otherwise, not bad really not blown away i'm afraid
- Zee.
I installed it. It works just as intended. Then I uninstalled it. Not my cup of tea. But it works great and the installation was flawless.
- MVB (Curmudgeon of FF)
Love that notifier.
- Francine Hardaway
...it seems to work best--and less noisily--if you make a list of favorite FF content (people and/or rooms) and set the notifier to that...
- .LAG liked that
I keep meaning to ask people what they're going on about a FriendFeed notifier. Installing this as soon as I get home.
- Jandy, ConcertMaven of FF
who's running old google deskbar?
- John Fu
Yeah I'd love to use it but Air is a resource hog I just can't deal with.
- EricaJoy
Another thought, I think the X button on the top right could be bigger. I seem to be accidentally opening liks quite a bit when I'm trying to close the pop up.
- Andrew
No, not yet - thank you for the reminder
- Susan Beebe
No, I haven't yet, quit nagging. ^_^
- Ron Bailey
I did, and promptly removed it after getting pop-ups every second.
- Mathew™ one of a kind
My ADD ass wouldn't be able to handle the distraction.
- Brad Williamson
would be like @_@
- Will Higgins™
I like it on my 24" display, but not on the 10" EEEPC. Long (vertically) messages aren't displayed very well at 1024x600
- Brian Daniel Eisenberg
Just tried to install it but the link doesn't open anything. Strange (XP w/ Firefox)
- Keith - @tsudo
Used compiz to make some adjustment to opacity, gamma values of the friendfeed notifier and now it is as sexy as jaunty native notifier
- Zaki Manian
That guy's a rafa benitez clone. Amazing
- Martin Liechti
from fftogo
Somebody should do one with Silverlight 3 (beta) with out-of-browser -support. That I could try :)
- Jemm
Martin, yeah I've noted this before, hehe. :-)
- Kol Tregaskes
Yes and I've made some observations and suggestions here: http://friendfeed.com/e...
- Kol Tregaskes
Yes, but don't really keep it on. The sheer amount of activity is so high that notifier is a major distraction from whatever I am doing. I only turn it on when I'm browsing FF fulltime.
- Parth Awasthi
I need another popup like a hole in my head.
- TranceMist
Not really interesting. Friendfeed is getting kinda boring tbh.
- Spencer
it's the dreaded ADOBE AIR. avoid it like the plague! :)
- Zio Bonino
Notifier without actual interface=useless to me.
- timedalkat
from twhirl
Just installed it but notifiers without filtering options = popup hell
- MiaD
I like it. It's like the real-time feed without having to take up a whole tab or sidebar. But I could never have it active at work - far too distracting. At home when I can keep an eye down in the corner while doing other things, it's great.
- Jandy, ConcertMaven of FF
I have. And I like it so far
- Martin Liechti
from fftogo
its great!
- Luigi Centenaro
In pop up heaven - how am I supposed to do any work?
- Jan Simmonds
不错的小工具，赞
- 阿石
Tried it, liked it but prefer the IM / XMPP interface, that doesn't cost me CPU since I already have a client running, and also gives me more control over the level of distraction.
- Robin Barooah
My first impression? I "like" much!
- Karoli
I tried it and it's fun but I realized that all the real-time-ness I need I get from the real-time view in a separate window without the distraction.
- Sam Grover
Semantic Enrichment of the Scientific Literature 2009 (SESL 2009) -- end of the month at the EBI. Looks like the kind of thing some people here would be into - http://www.ebi.ac.uk/Rebholz...
Richard Akerman, Richard Klancer, Sean McBride and 9 other people liked this
This workshop will focus on semantic enrichment of the scientific literature. To this end, workshop participants will have the opportunity to hear about and discuss solutions that capture information from the authors directly and that deliver documents with their annotations. Furthermore, we will discuss the needs of different user groups for the benefits from the scientific literature...
more...
- Duncan Hull
This looks very interesting. Duncan how are you involved? Anyone else going to attend? I am going to try to get NextBio to send me :)
- NextBio
@NextBio a colleague of mine (Sophia Ananiadou) is presenting, but I probably won't go as it clashes with something else...
- Duncan Hull
I've just registered
- Andrew Clegg
MGH to use genetics to personalize cancer care - The Boston Globe - http://www.boston.com/news...
Sally Church, Andreas Matern and Brad Chapman liked this
I'm looking for a semi-automatic way to associated genes with pathways/interaction data. Ideally, my scripts dump a gene list out, (either to file, or to an API), and the program shoots back relevant pathways (and maybe enrichment scores). Any suggestions?
Eric Bardes, Pawel Szczesny, Jason Winget and 5 other people liked this
I know of DAVID for GO scores, but I'm looking for something that does pathways too, and can handle fairly large volumes of data
- Chris Miller
Blast2Go will map your genes to GO terms and then to pathways from KEGG. May be worth a quick look to see if it will do what you want.
- Andrew Perry
Does NextBio do anything like this? I think you have to register but maybe that is free
- Shirley Wu
GSEA? (http://www.broad.mit.edu/gsea...) I believe you can download both the program and their curated list of pathways. If I recall the paper right, I think they've chosen a rather odd test statistic, but judging by its citation history, that clearly that hasn't stopped many people from using it...
- Andrew Su
Try e.g. http://www.uniprot.org/uniprot.... Could expand this into and "or" query if you don't have hundreds of genes, but repeating the query for each gene is probably simpler. Add pathway:* or interactor:* to the query to remove matches that don't have either.
- Eric Jain
I have done something similar for a set of genes from Drosophila using pathway data from KEGG. After getting pathway information for the list, I calculated enrichment using custom scripts.
- Khader Shameer
Yeah, Khader, I could download KEGG or one of the other DBs, but I'm hoping for something off-the-shelf and easy. Thanks for the suggestions, all - I'll start checking them out.
- Chris Miller
For interactions, you can use STRING (http://string.embl.de) and its API (http://string-stitch.blogspot.com/2008...). For pathways, try iPath (http://pathways.embl.de/).
- Michael Kuhn
You could try signing up for a demo account at commercial provider Ingenuity (http://www.ingenuity.com/) - you only get two weeks to crunch your data before you have to resubscribe with a new email account (and lose all your analysis), but it has the best functional annotation and interface I've found so far.
- Daniel MacArthur
If you have a UniProt accession or ID for your gene, you can try sending it to my PHOG server, like this: http://phylofacts.berkeley.edu/ortholo.... This gives you a report including KEGG sequences and protein-protein interactions of the query sequence and its orthologs and in-species paralogs. If you want CSV, go instead to http://phylofacts.berkeley.edu/ortholo.... We...
more...
- Ruchira S. Datta
DAVID does do pathways (KEGG and Biocarta). You could try ToppGene, which detects enrichment based on a number of features: http://toppgene.cchmc.org/
- Walter Jessen
Bioinformatic challenges for the next decade(s) - Journal Article - http://journals.royalsociety.org/content...
Andreas Matern, Jon and Tom Walsh liked this
The science of bioinformatics has developed in the wake of methods to determine the sequences of the informational macromolecules—DNAs, RNAs and proteins. But in a wider sense, the biological world depends in its every process on the transmission of information, and hence bioinformatics is the fundamental core of biology. We here give a consideration of some of the key problems of bioinformatics in the coming decade, and perhaps longer.
- Khader Shameer
from Bookmarklet
FreeMat is a free environment for rapid engineering and scientific prototyping and data processing. - http://freemat.sourceforge.net/
Deepak Singh, Daniel Mietchen, Khader Shameer and 13 other people liked this
This is similar to commercial systems such as MATLAB from Mathworks, and IDL from Research Systems, but is Open Source. FreeMat is available under the GPL license.
- sofarsoShawn
from Bookmarklet
I've never seen Matlab/Freemat working. Can it be described just as a GUI over 'R' ?
- Pierre Lindenbaum
What is the difference to Octave?
- joergkurtwegner
@Joerg: It's in the FAQ: http://freemat.sourceforge.net/faq... "Who said choice was a bad thing?" :-)
- Pierre Lindenbaum
@Pierre, right, see also http://tinyurl.com/math-os-1o1
- joergkurtwegner
I don't do a lot of Matlab, but I'm glad to see projects like this going strong. The world needs high-quality, open source Matlabs and Mathematicas. Here's hoping it's as successful as R is some day.
- Chris Miller
This is in the standard Ubuntu repository. Just do a sudo apt-get install freemat.
- imabonehead
This is pretty neat, has anyone tried this? I'm curious about its performance and numerical accuracy. I know MATLAB is supposed to have some super-special matlab-fu to enhance its performance as well as proprietary algorithms for their PDE solvers -- does this match up?
- Benjamin Tseng
Barack Obama: The 50 facts you might not know - http://www.telegraph.co.uk/news...
Kevin Barrow, Andreas Matern, Tim Ostler and 2 other people liked this
moving my development machine from Vista to OS X
dK, Andreas Matern, Rajarshi Guha and 3 other people liked this
Thank God you're a man - http://pixdaus.com/single...
Ming Tsai, amelia arapoff, Rob Hoeting and 12 other people liked this
haha
- Ross Miller
from Bookmarklet
they know Mike.....
- amelia arapoff
PubChem WTF #1 - http://depth-first.com/article...
Richard Akerman, Andreas Matern, Michael Kuhn and Neil Saunders liked this
Ha, not quite chickenwire, but close :) See http://en.wikipedia.org/wiki...
- Egon Willighagen
there are lots of them: http://www.ncbi.nlm.nih.gov/sites... PubChem blames ChemSpider, but this doesn't even load for me: http://www.chemspider.com/Chemica...
- Michael Kuhn
so-called "data integration" is nothing more than matching multiple IDs from different databases...
Euan, Andreas Matern, Daniel Swan and 5 other people liked this
That 'like' link should be called 'agree'. I agree, but don't like it.
- Jan Aerts
'The Reactome Book' - "A textbook of biological pathways" (3252 pages - free PDF) - http://www.scribd.com/doc...
Pawel Szczesny, Wubin Qu, imabonehead and 5 other people liked this
"European Bioinformatics Institute & Cold Spring Harbor Laboratory The contents of this book may be freely copied and distributed in any media, provided the authors, plus theEuropean Bioinformatics Institute and the Cold Spring Harbor Laboratory, are credited".
- Graham Steel
It's also a website: http://reactome.org/
- Todd Harris
Thanks Todd - I didn't know that.
- Graham Steel
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