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Rob Syme › Comments

Rob Syme
9 September 2011 - Dr Jens Berger - http://robsyme.com/9-septe...
Posted via email from robsyme - biolateral - Rob Syme from Posterous
Rob Syme
Tutorials (2011 version) — ANGUS v2.0 documentation - http://ged.msu.edu/angus...
A neat set of tutorials if non-informatics biologists ask for a broad introduction to NGS analysis. - Rob Syme
aydın
a is not b but p is q, guess why
isequal.png
@mirat, i m not sure, basically "is" is not for equivalent, it is for object identification but the strange thing is why it differs - aydın
yeap the point is python caches small ints (till 256) and when you define an int it returns cached small int object so "is" comparasion passes but after 256 python creates new object and "is" failed, thanks to ahmet :) - aydın
Extra credit, explain: p=1000; q=1000; p is q - Rob Syme
Every code object has a tuple of constants. The LOAD_CONST opcode loads a constant from this tuple onto the VM stack. So every time 1000 occurs in the program text, it refers to the same object in the tuple of constants for that block. At an interactive interpreter, each line is its own block. You can put multiple simple statements in one statement with semi-colons, so here you've... more... - Jeremy Hylton
it is clearer for now, thanks jeremy - aydın
thanks for this feed - amir
Paul J. Davis
I haven't seen anything pop up on Convore so I thought I'd mention it. Its somewhat like friendfeed but also different. https://convore.com/
Very conversations based, but doesn't seem to aggregate anything. Everything has to be a typed message, right? - Rob Syme
That said, it's ridiculously easy to automate posting via the API. https://gist.github.com/816542 and convore.com/api/ - Rob Syme
Its definitely missing the built-in aggregation stuff. I haven't heard them talk about adding those types of features but its only been public for a couple days so I reckon anything could happen. - Paul J. Davis
Rob Syme
Applying some time-consuming program/script to each entry in a fasta file? Check out the new version of GNU parallel: http://www.youtube.com/watch...
Applying some time-consuming program/script to each entry in a fasta file? Check out the new version of GNU parallel: http://bit.ly/f5hihw
Play
... making embarrassingly parallel problems embarrassingly easy to parallelize. - Rob Syme
Rob Syme
Are Hilbert plots intuitive enough for a genomics paper? Blue are the genes on reference strain A, red is read coverage (of A) by strain B, green is read coverage by strain C. (http://en.wikipedia.org/wiki...)
scaffold_2_10.png
Hilbert plots? Plots of which the width and height can be determined, as well as squareness? - Egon Willighagen
I should have said "plots of Hilbert curves". The wp link has a good description. Used for visualising a long vector in 2d space. The take-home message of the figure is that genes are missing in 'chunks'. Do you think that this is apparent from the pic above? - Rob Syme
I think the image indeed nicely slows blocks where something is 'wrong'... you mentioned the different colors for different strains... but looking at the random color distribution, I do not really understand how to read that bit... then again... those interesting 'blocks' do show a color tendency... is that what I should read from the plot? - Egon Willighagen
Yep, you've got it. The different colours appear when more than one strain is present (blue + red => purple, green + blue => yellow, etc). Thanks for the feedback Egon. Much appreciated. - Rob Syme
Pierre Lindenbaum
In GMail, "Reader" has been replaced by "Photos".... :-/ (via @TechCrunch )
and now it seems to be back again. Strange. - Rob Syme
Clojure
JRuby/Clojure integration - http://www.reddit.com/r...
Doesn't feel particulaly practical at the moment, but I'd be very happy to be proven wrong. - Rob Syme from Android
Rob Syme
The Qlobe: A Spinning Globe in a Ruby Quine - http://www.rubyflow.com/items...
Wow. To top it off, passing an integer x as an argument spins the globe x degrees. - Rob Syme
Deepak Singh
There was bioinformatics in 1902 http://ngrams.googlelabs.com/graph...
I think there might be an error in some of the dating - http://bit.ly/dPP27w - Rob Syme
It was amusing to see that little peak. But fascinating to see all that data - Deepak Singh
Rob Syme
My saliva (and my friend's, and my professor's) is @23andMe bound! Thanks @shwu!
I have to do mine. This weekend - Deepak Singh
@Neil. We thought we'd save on shipping ;) - Rob Syme
Rob Syme
Inaugural BioRuby IRC Conference: Sunday, Dec. 19, 2010, at 23pm JST (Japanese Standard Time). Details here: http://lists.open-bio.org/piperma...
Pjotr Prins has suggested that people might like to give some talks via video. Make some noise on the mailing list if you want to join in - bioruby@lists.open-bio.org - Rob Syme
Lars Juhl Jensen
Medical researcher discovers integration, gets 75 citations « An American Physics Student in England - http://fliptomato.wordpress.com/2007...
Most recent citation? 2010 - Rob Syme
I can't believe it! - Björn Brembs
Rob, cito:usesMethodIn or cito:disagreesWith ? - Egon Willighagen
@Egon that's a good question. I was being a bit dramatic. The recent citations are pro, but they recognise the paper for what it is. Eg: "Glucose tolerance was estimated as the product of the areas under the curve (AUCs) for glucose and insulin calculated using the trapezoidal method (30), with higher AUCs indicative of reduced glucose tolerance" - Rob Syme
Ack, taking that paper as a tutorial... that make sense. - Egon Willighagen
Rob Syme
A cool job at a great university in a boring city. - Rob Syme
Rob Syme
Watched biologists' eyes glaze over on a talk on expectation maximization and mixed models.
Mmmm, glazed eyeballs, delicious. And now I have a recipe! - Bill Hooker
Ha! We certainly have a surplus of the raw ingredient here, Bill :) - Rob Syme from email
Shirley Wu
The perfect gift for the genetics geek, genealogy buff, or science nerd that you know (or maybe just for yourself ;) - get 23andMe for $99 today and tomorrow using this discount code ($400 off regular price): UA3XJH (https://www.23andme.com/store...)
Whats with the new $5 per month subscription ? :) I was going to buy a bunch for xmas gift but this might put me off a bit. - Pedro Beltrao
Dropping the base price to $99 requires us to collect additional revenue, unfortunately. Think of it as a $159 gift? with option to continue? We continuously update the content so there it's not a one-time value. - Shirley Wu
Can that be canceled any time? - Rachel Walden
@Shirley - sure, it is still a great gift. - Pedro Beltrao
I think I may buy this as a christmas present for someone. I will be sure to point them towards the store page showing the full price. - Michael Barton
@Rachel, there is a 1 year minimum at purchase but it can be canceled anytime thereafter - Shirley Wu
Thanks, Shirley - Rachel Walden
Thanks Shirley! Just ordered mine. - Rob Syme
Ordered mine, blogged and tweeted about it, and now pondering whether a Barcamp-style meeting makes sense once Genomes Unzipped allow data contribution. Sigh :-) - Oliver Hofmann
also add ~$90 to the cost in case of international shipping - Attila Csordas
Andrew Perry
Bronze medal for Monash #iGEM2010 .. stoked! Congrats to all teams !
Congratulations! - Rob Syme from Android
Thanks Rob - it's been a seriously busy year for me helping advise these guys, but they worked really hard and deserved to be rewarded. Not a bad result for a n00b team. - Andrew Perry from Android
Do you know if any WA universities put a team together? - Rob Syme
There haven't been any WA teams in the past, and I havent heard any plans, but the way iGEM teams pop up organically someone may be starting one for 2011 and we wouldn't know. I was surprised Oliver Rackham didn't initiate something when he returned to Australia - seems right in his area of interest. - Andrew Perry from Android
Rob Syme
Off to Canberra for my first 'real' presentation as a PhD student. *Very* nervous.
Thanks Neil. It went well. Very exciting to be part of a conversation where papers from 2008 are considered ancient history :) - Rob Syme from Android
Rob Syme
Wow. Very cool R. - Rob Syme
Rob Syme
BEDTools version 2.10.0 - http://seqanswers.com/forums...
The always handy BEDTools gets even more convenient. - Rob Syme
Pierre Lindenbaum
Geospatial Indexing in mongo http://www.mongodb.org/display... anyone tested this with genomic coordinates ?
I've been pondering the same question, but I haven't thought of a good use for the second dimension. If latitude is ignored, would there be any advantage over indexing the position? - Rob Syme from Android
Thomas Mailund played with this kind of geospatial queries with MySQL http://www.mailund.dk/index... - Pierre Lindenbaum
Actually: the MongoDB people would be really interested in working together with the bioinformatics community. Didn't have time to discuss this at length with them after my talk at MongoUK, but did promise to stay in touch about it. Putting this back on my todo-list. - Jan Aerts
Deepak Singh
The Graph Traversal Programming Pattern - http://depth-first.com/article...
Very cool. I wonder what sort of performance gains might be made by storing genomic feature graphs (eg: http://gmod.org/wiki...) in a graph db like Neo4j. It might just be that the graphs aren't deep enough to warrant a shift from relational stores, but probably worth a look. - Rob Syme
Pierre Lindenbaum
Dalliance, an interactive browser-based client for genomic DAS http://www.biodalliance.org/
Cool! Snappy svg rendering, local storage for persistent sessions. Seems like a better approach than jBrowse - Rob Syme
Rob Syme
Protocols for distribution of large genomic datasets - Rob Syme
Andrew Perry
Watching the BRCA 'gene patenting' report on #4corners, ie Myriad vs ACLU
thanks for the heads-up. - Rob Syme
No probs. There's always iView if you jumped in half way too. - Andrew Perry from Android
Rob Syme
Intel And Nokia Ready Assault On Mobile 3D - http://www.gizmodo.com.au/2010...
You have got to be joking. - Rob Syme
Rob Syme
RIP Prof John de Laeter. The first West Australian giant of science and a man instrumental in the foundation of @scitechwa
Oops, didn't mean that 'first' to be in there. Certainly still a great West Austalian. - Rob Syme from Android
Rob Syme
Fatvat: JVisualVM and Clojure - http://www.fatvat.co.uk/2009...
JVisualVM is a Java Virtual machine monitoring tool that allows you to see a live view of the Java memory, cpu and threads that are currently active. In this post, I'll look at how easy it is to profile Clojure code using JVisualVM. - Rob Syme
Rob Syme
GitHub stats with Incanter - http://citizen428.net/archive...
Variations on a theme - Rob Syme
Rob Syme
genoPlotR: comparative gene and genome visualization in R - http://bits-ngs.blogspot.com/2010...
Can't wait to try this out next week. - Rob Syme
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