NorahDesk
non-coding RNA detection from deep sequencing data
NorahDesk is a small non-coding RNA (ncRNA) detection tool for RNA sequencing (RNA-Seq) data, developed by my PhD student Chikako Ragan.
NorahDesk utilizes the coverage-distribution of small RNA sequence data and thermodynamic assessments of secondary structure to reliably predict and annotate ncRNA classes.
For more information visit the webpage.
All you need is … a ticket to this year’s TEDxBrisbane convergence.
Looking forward to meeting new people !!
I am one of the three finalists for this year’s Infotech Research Award from Women in Technology (WiT). This is a particularly great honor because the other two finalists are Prof. Janet Wiles and Sandra Mau. I’m looking forward to a wonderfully inspiring evening at the gala dinner of the 14th annual WiT awards.
+++ UPDATE +++
Prof. Janet Wiles won … congratulations !!
image by lorns (#witawards)
Triplexator is a bioinformatics tool (by Fabian Buske) harnessing the power of a so far underutilized mechanism for sequence-specific DNA binding that is of great interest for biotechnological and gene-therapeutic applications.
This potent homing mechanism is provided by nucleic acids triple helices, also called triplexes, which are oligonucleotide complexes made of three strands of either DNA or RNA, originally described by Felsenfeld et al. [J. Am. Chem. Soc. 1957] and reviewed earlier this year [Buske et al. RNA Biology 2011].
Triplexator enables to study all aspects of nucleic triplex formation, i.e. (i) identify triplex-forming oligonucleotides (TFOs) in single-stranded nucleic acids, (ii) identify suitable target sites (TTS) in double-stranded sequence and, most importantly, (iii) assess the compatibility of the two participating partners according to canonical triplex formation rules (TFO/TTS pair).
More here.
I am organizing QBI’s bioinformatics seminar series to give researchers a better understanding of bioinformatics, specifically with respect to second generation sequencing data production and analysis. By the end of the seminar series the researchers should have a better understanding of time frames, analysis steps and the research contribution that they can expect from the bioinformatics analysis for their projects.
Along with the seminar series, there will be a “walk-in-clinic” set up where you can ask bioinformatics questions and get some of the smaller tasks solved directly.
The seminar series and subsequent “walk-in-clinic” will be Thursdays 10am starting from the 16th June. More details on the CBG-webpage.
From Esteban Moro Egido blog "publish and perish"
Russ Altman from Stanford University has recently reviewed and presented the most interesting bioinformatics papers from 2010. While this is undoubtedly very subjective (obviously, because he did not mention any of my papers), it is an excellent practice and should be done in any research institute for all the topics that are of interest to this community. Staying informed about what actually is the cutting edge science, is paramount for real progress, rather than keep on using the same old hat, and being frustrated that the outcome never looks promising.
Speaking of promising, I particularly like a paper titled “Over-optimism in bioinformatics research.” that features in this “highlights of 2010″ list, which summarizes some of the things that are seriously wrong with the research community as a whole (not just bioinformatics): negative results are not easily publishable, this seduces “authors to find something positive in their study by performing numerous analyses until one of them yields positive results by chance, i.e. to fish for significance”. Also, positive results are all too willingly accepted while negative results are interrogated until they crack and pretend to be positives just for the publication. We all know that being a significance-fisher does not require too much interrogation skill because the evil sidekick “noise” is abundantly present in the types of data most of us work with. Contributing to this is the fact that most results are not reproducible once they are published. This I blame on unavailable code, software version changes, reference data update but most of all on the mad rush that is applied during data production and analysis because one might get scooped.
This brings us full circle with why a review of current research activity, “highlights of 20XX”, is paramount: knowing what others do gives us a better chance to position our research in an area that is truly new and unique, which means we have more time to form a solid hypothesis, do good science and then publish high confidence results only (positive or negative). However, the current “publish or perish” attitude makes this approach career suicide. But, there could be a shift towards “more quality than quantity” if the reviewers are briefed by their institute’s “highlights of 20XX” presentations to scrutinize bad science. So, since we are all reviewers at some stage, we can start making the first step towards good science at our next review ourselves.
My formal education is over, life can start now! A big thanks to everyone who helped along the way.
We are organizing a special topics workshop titled “The successes, challenges and prospects for GWAS mega-analyses for complex diseases“, which is part of this years’ International Conference on Systems Biology (ICSB2010).
The program features a fantastic list of high profile researchers from a wide range of disciplines and institutes around the world. The workshop will create a productive environment, where new collaborations are formed and new experimental setups discussed.
Please visit the workshop’s web page for more details of the program and information how to register.
by mithrandir3
Amazon’s e-book reader, Kindle, has just become a whole lot more convenient, not for the owner that is, but for steering the stupid masses towards the good of humanity. By deleting sold e-books from the Kindle devices due to copyright-issues of the digital publishers, Amazon has “generated waves of online pique” according to The New York Times. Although Jeffrey P. Bezos, the founder and CEO of Amazon, apologized later for deleting the illegally sold copies of the e-books in a forums discussion entry and called the ” ‘solution’ to the problem [..] stupid, thoughtless, and painfully out of line with our principles”. It might have been an action free from censorship ambitions, but it shows that the mechanisms are in place to eliminate unwanted books.
Books are “a pleasure to burn. It [is] a special pleasure to see things eaten, to see things blackened and changed.” as Guy Montag, the “fireman” in Farenheit 451, knows. But the act of burning books in reality is generally less pleasurable because widely unaccepted and very unpopular these days. How convenient that the new technology can make books “disappear” clean and easy, without huge arguments by the hysterical book-owner, without even being there. Remotely and and with full refund can books be dropped down the memory hole – book burning v2.0.
But why burn them? Burning implies nasty things about an increasingly censorship-hungry “system” and does not make creative use of the associations we have with books to begin with. Why not instead tweak the content of a book as desired and bring the past up-to-date as suggested by Nineteen Eighty-Four (incidentally one of the books deleted). Books still have a status of trustworthiness, in our minds they are a silent witness of the invariable truth of our collective memory because once published the content did not change. Well, that’s all in the past that is. Nowadays, Amazon updates books without warning to bring them up-to-date to the newest edition. If this new edition removes spelling errors or adjusts the content to a more … can not be controlled. As rrabbit noted, if Amazon wants “Oceania [is] at war with Eurasia: Oceania had always been at war with Eurasia” until tomorrow when Amazon updates the books to say that Oceania had always been at war with Eastasia instead and that Eurasia is our trusted ally — has always been. The need to burn books has ceased to exist (if it ever had in the first place), because undesirable content can be rewritten on-the-fly — embrace book burning v3.0, made possible with Kindle.
But it is not the technology that is evil, the effort of saving trees and gallons of fuel by distributing books online must be applauded and so the aim of providing editing-error free books. Even the act of deleting illegally sold books is not shocking in itself, if Amazon would have knocked on every buyers door and would have swapped the illegal copy with a legal one from a different publisher, no-one would have second guessed Amazon. But it is the combination of technological possibility and questionable intentions or judgements of a company that lets the darkest dystopian fiction seem plausible: who would not start to doubt ones mental health if facts start to dissolve before ones very own eyes.
Amazon has demonstrated of being capable to commit book-burning v2.0 if convenient (letting books disappear). They have the technology in place of burning books v3.0 (updating the content unnoticed). I am not convinced that Amazon has enough integrity to withstand the pressure of a government endorsed censorship to tweak the by then unwanted content. Next time when you hold a Kindle, be prepared to read nothing but government approved propaganda.
While I’m against illegal content on the web, an internet filter is not the solution.
