This JABBA-award winning software wants a shot at redemption

A new tool has been described in the journal Bioinformatics:

All of the words that contribute to the name of this acronym are right there in the article's title. But as this is a JABBA-award-worthy name, we don't expect each word to contribute its first letter (or only one letter):

REDEMPTION: REduced Dimension Ensemble Modeling and Parameter estimaTION

This is certainly far from being the most bogus bioinformatics acronym that I have seen and — as far as I can tell — the name is unique (within the context of bioinformatics). However, I am particularly wary of tools that use a short name which a) has no obvious connection to what the software actually does and b) has potentially emotive associations in other contexts, e.g. religion and/or politics.

Front Line Genomics interview with Illumina CEO Jay Flatley includes a question from me

Issue 5 of the Front Line Genomics magazine is now online (in PDF format). The latest issue includes a fascinating interview with Jay Flatley, CEO of a little sequencing company you may have heard of (Illumina).

Continuing their trend of allowing former interviewees to ask questions, I was lucky enough to have one of my questions chosen for the interview. Here is my (somewhat lengthy) question along with Jay's response:

KB: When Apple introduced the original iPod in 2001, it was an expensive luxury ($400) that went on to change an entire industry. Remarkably, by 2006 the iPod product line was Apple’s largest source of revenue. Today, you can buy a cheap iPod knock-off for less than $20 and iPods now account for <1% data-preserve-html-node="true" of Apple’s revenue. Smart phones have made dedicated music players largely irrelevant.

So here’s my question...is the Illumina of 2015 like the Apple of 2006? What does Illumina do when, in five to ten years’ time, everyone will be getting his or her genomes sequenced and analyzed in an automated manner for less than $100? If the HiSeq platform is Illumina’s iPod, what’s going to be your iPhone?


JF: That’s a great question! We certainly do believe in the 5-10 year time frame that the ability to sequence a genome will be available to everyone because the economics will be there and the clinical utility will be there. That will be an enormous market opportunity.

The first thing I would say is, unlike the iPod which became a commodity because the actual technology could be replicated by other companies – especially the physical interface, the headphone jack and storage inside the iPod. Sequencing is quite challenging by comparison. It requires the intersection of a dramatically larger number of technologies which all have to work together in quite a complicated and sophisticated way. Having said that, we think that our sequencers need to become easier to use, need to become faster, need to become cheaper.

These are all things we’re working on. We obviously can’t layout ourroadmap for people today, but there will be technologies beyond the HiSeq, and those technologies will ultimately enable people to sequence their genomes at much lower prices than $1,000. The trick for Illumina, of course, is to be the company that introduces that technology, and brings the equivalent of the iPhone that largely replaced the iPod to market and that we don’t let someone else do that before we do it.

The full interview starts on page 20 of the PDF, and you can access previous issues of Front Line Genomics magazine here.

Ewan Birney reflects on the use of twitter and blogging for science communication [Link]

Worth reading. Ewan includes some comments regarding the growing use of pre-print platforms:

Blogging is nice, because it is accessible to a broader audience and allows for a more chatty, 'natural language' style – but if the main purpose is to communicate with scientists, pre-publication servers are a better way to go

Ewan singles out arXiv, bioRxiv, and F1000Research, but I think PeerJ are also worth a mention here. They also have their own pre-print server and they also encourage open peer review.

Additionally, I think figshare is another outlet that can be used for dissemination of science material that may not suitable for a peer reviewed publication. One cool thing about using figshare for posting preliminary data or commentary pieces is that articles are allocated a DataCite DOI and can therefore be cited.

BioNano Genomics are holding a webinar on October 12th about 'Hybrid Scaffolds' [Link]

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The Irys platform by BioNano Genomics seems to be a useful tool by which to help assess the completeness and contiguity of genome assemblies. I noticed today that they are holding an webinar which may be of interest some of the readers of this blog. From the webinar registration page:

Please join us for our Hybrid Scaffold webinar. We will discuss the applications of the software, which include the building of longer contigs, validation of existing contigs, and acquisition of novel map level information. Experimental design considerations will be reviewed for ideal data integration. We will walk through each stage of Hybrid Scaffold troubleshooting data optimization and pointing out files of interest.

 

Financial disclaimer: I do not own shares in any biotechnology company.