bionics.it
Random links from the Hadoop NGS Workshop | Bionics IT
http://bionics.it/posts/hadoop-ngs-workshop
Random links from the Hadoop NGS Workshop. Share this on → Twitter. Posted on: 19 Feb '15. Some random links from the Hadoop for Next-Gen Sequencing workshop. Held at KTH in Kista, Stockholm in February 2015. UPDATE: Slides and Videos now available. By Big Data Genomics. Tweet by Frank Nothaft on common workflow def. Part of Global Alliance for . Another link is ga4gh.org. Does support multiple outputs etc. Black-box vs. White-box. Workflow dependency graph can be dynamically built up while you're running.
bionics.it
Dynamic Navigation for Higher Performance | Bionics IT
http://bionics.it/posts/dynamic-navigation-for-higher-performance
Dynamic Navigation for Higher Performance. Share this on → Twitter. Posted on: 11 Mar '15. Improving performance in Delphi Bold MDA applications by replacing navigation code with derived links in the model. Guest Post on Model Driven Architecture. This post was originally posted on HowToDoThings.com in 2002. Some feedback and further discussion on this post is available in this thread. But with Bold you can often directly address unnecessary link navigation, the redundant navigational code/ OCL. But I'm ...
bionics.it
NGS Bioinformatics Intro Course Day 1 | Bionics IT
http://bionics.it/posts/ngs-intro-course-day-1
NGS Bioinformatics Intro Course Day 1. Share this on → Twitter. Posted on: 9 Feb '15. Just finished day 1 of the introductory course on Bioinformatics for Next generation sequencing data. At Scilifelab Uppsala. Attaching a photo from one of the hands-on tutorial sessions, with the tutorial leaders, standing to the right. Today's content was mostly introductions to the linux commandline in general, and the UPPMAX HPC environment. Anyways, in the time between student questions, I also browsed around on a v...
saml.rilspace.com
Reasoning | Samuel's Tech Blog
http://saml.rilspace.com/tags/reasoning
Samuel's Tech Blog. Log in / Create account. 3rd Project Update (Integrating SWI-Prolog for Semantic Reasoning in Bioclipse). Thu, 2010-04-08 14:17 by Samuel Lampa. I just had my 3rd, and last project update presentation (before the final presenation on April 28th), presenting results from comparing the performance of the integrated SWI-Prolog against Jena and Pellet, for a spectrum similarity search query. Find the sldes below. Samuel Lampa's blog. Chemical ring and cage structures need rules (seemingly).
blipkit.wordpress.com
memoization+persistence | Blip Blog
https://blipkit.wordpress.com/2010/06/08/memoizationpersistence
Logic Programming in Biology. The mis-named “tabling” module (should really be called “memoize”) now allows for persisting memoized calls to a file. See:. Http:/ github.com/cmungall/blipkit/blob/master/packages/blipcore/tabling.pro. Docs up on the pldoc server soon). To see how this works, consider the transitive closure of the subclass/2 fact, as defined in the ontol db schema:. SubclassT(X,Y):- subclass(X,Y). SubclassT(X,Y):- subclass(X,Z),subclassT(Z,Y). Init :- table pred(ontol db:subclassT/2). After...
bionics.it
The smallest pipeable go program | Bionics IT
http://bionics.it/posts/smallest-pipeable-go-program
The smallest pipeable go program. Share this on → Twitter. Posted on: 18 Dec '14. Edit: My original suggested way further below in the post is no way the "smallest pipeable" program, instead see this example (Credits: Axel Wagner. Package main import ( "io" "os" ) func main() { io.Copy(os.Stdout, os.Stdin) }. Or (credits: Roger Peppe. Package main import ( "bufio" "fmt" "os" ) func main() { for scan := bufio.NewScanner(os.Stdin); scan.Scan(); { fmt.Printf("%s n", scan.Text() } }. At those rare occasions ...
bionics.it
Links: Our experiences using Spotify's Luigi for Bioinformatics Workflows | Bionics IT
http://bionics.it/posts/our-experiences-using-spotifys-luigi-for-bioinformatics-workflows
Links: Our experiences using Spotify's Luigi for Bioinformatics Workflows. Share this on → Twitter. Posted on: 12 Feb '15. Fig 1: A screenshot of Luigi's web UI, of a real-world (although rather simple) workflow implemented in Luigi:. Update May 5, 2016:. Most of the below material is more or less outdated. Our latest work has resulted in the SciLuigi helper library. Which we have used in production and will be focus of further developments. Wrote a small helper library, "luigi's monkey wrench". A nice p...
bionics.it
FBP inspired data flow syntax: The missing piece for the success of functional programming? | Bionics IT
http://bionics.it/posts/fbp-data-flow-syntax
FBP inspired data flow syntax: The missing piece for the success of functional programming? Share this on → Twitter. Posted on: 16 Jul '15. Have added link to a working example in Go(lang), of the final non-working python example code. See this follow-up post with the Go example. See especially this excellent comment. In the Reddit thread. See also discussion on Reddit. See also discussion on Hacker News. See this discussion on twitter. About combining data from multiple ports. FBP) or Data Flow. There a...
bionics.it
NGS Bioinformatics Course Day 3: New Luigi helper tool, "real-world" NGS pipelines | Bionics IT
http://bionics.it/posts/ngs-bioinformatics-intro-course-day-3
NGS Bioinformatics Course Day 3: New Luigi helper tool, real-world NGS pipelines. Share this on → Twitter. Posted on: 3 Mar '15. It turned out I didn't have the time and strength to blog every day at the NGS Bioinformatics Intro course, so here comes a wrap up with some random notes and tidbits from the last days, including any concluding remarks! These days we started working on a more realistic NGS pipeline, on analysing re-sequencing samples ( slides. First some outcome from this tutorial. This result...
SOCIAL ENGAGEMENT