One thing system biologists want is to have by and large absolute protein concentrations or copy numbers per cells available cheaply for their models leveraging all sorts of omics data. Looks like such results can now be easily delivered based on a study published on the 15th of September by the Mann lab in Molecular & Cellular… Continue reading Changing the game: absolute protein quantification by relating histone mass spec signals to DNA amounts and cell numbers
1. DNA methylation age of human tissues and cell types by Steve Horvath: This is the type of relevant data mining study most bioinformaticians are dreaming of: you pull together a large body of publicly available datasets (CpG methylation) that are not too heterogeneous (Infinium type II assay on Illumina 27K or Illumina 450K array platform), derive robust… Continue reading Three links in Aging, Regenerative Medicine & Healthy Lifespan Extension: 17 December 2013
Sage Bionetworks is a not-for-profit organization developing an open-access “pre-competitive” platform for networked and annotated models of human disease. It’s a huge and unparalleled bioinformatics enterprise: starting with an anonymous $5 million donation and soon making high throughput, large-scale human and mouse biological data (largely from Merck) available in the range that’s already in the… Continue reading Sage Bionetworks Update: building an OA standard for human disease biology
There is a nice initiative now in Budapest dedicated to the present and future of high technology: a new private university momentarily dubbed as Aquincum Institute of Technology (AIT) will be built near to the Graphisoft Park in Óbuda (Aquincum) concentrating on competitive information-/biotechnology (mainly bioinformatics) education and entrepreneurship. The main instigator of the project… Continue reading Aquincum Institute of Technology, Budapest, IT & BT shaking hands
I argued many times here that biology based biotechnology is the next information technology but in order to do so, biotech should harness good IT patterns and mimic its massive computing practices to handle the enormous amount of constantly accumulating data. Often this trend could be summarized in a simple way: keep your eye on… Continue reading Petabyte Age Wiredesque lesson on what science can learn from Google
As of this moment the population of The Life Scientists Room on FriendFeed is 73. See the BioGang in motion and get an initial statistics on the distribution of wet lab/dry lab, academic/industrial people there. Here are the first 8 answerers out of the 16 so far.
“I feel like I am talking to an empty room. Why do I feel like I am talking to an empty room?” starts Michael Marron his Google Tech Talk on NIH and the computational infrastructure for biomedical research rather unfortunately. (I remember that room.)
It seems that my favorite ever unconference, the SciFoo Camp will be aroundunconferenced by a BioBarCamp this year. The whole idea of the BioBarCamp is based upon the SciFoo Camp, so it is by no means a competitive but a complimentary event. From the BarCamp wiki: “The BioBarCamp is an idea (fed by the tweets… Continue reading BioBarCamp in the Valley before the SciFoo Camp!
In order to have the slightest change to design a robust, systemic life extension technology, we need to accumulate every systemic macromolecular, cellular, tissue- and organ level data of the normal, physiological human body, connect the trillions of nodes with scalable software algorithms and suck out the draft of the proper sequence of consecutive treatment/regeneration… Continue reading Human proteome project: 21000 genes/1 protein, 10 years, $1 billion?
At the SciFoo Camp last year at the Googleplex I suggested a little unconference session (ok, there were some slides ready on my MacBook) and one participant was Chinh Dang (another was this inventor) Technology Director of the Allen Institute for Brain Science who made a little intro to the work of the Institute to… Continue reading Blow your Brain Explorer out with the Human Allen Brain Atlas!
The current operational idea behind Google’s Palimpsest Project is to ship 3TB (terrabyte= 1.0995 x 1012 bytes) drive array (Linux RAID-5) for scientists, who upload their data and FedEx the hard drives back to Google. Google then make those data publicly available and manageable. This file transfer method was heavily criticized by Dai Davies in… Continue reading How much data is produced by a life scientist/day?
IT people are the dominant high tech tribe today and especially on the web. But biotechnology (BT) is the next infotech so no wonder that the IT crowd is growingly curious about everything biotagged on the one hand, while they are usually not too savvy in DNA-RNA-protein-organelle-cell-tissue-organ-organism related matters on the other hand. Check for… Continue reading Let’s compile a Biotech for IT folks book and publish it!
For historical reasons the standard human mitochondrial sequence, the Revised Cambridge Reference Sequence (rCRS) is a reconstruction of a single European individual’s mtDNA and contains several rare alleles. That’s why many times a usual mtDNA sequence alignment must appeal to phylogenetic historical reconstructions. The rCRS nevertheless provides a uniform nucleotide numbering scheme (0-16569). On the… Continue reading The human mitochondrial consensus genome sequence by Robert Carter
Your 16569 basepair long human mitochondrial genome does a lot for you and tells a lot about you. It encodes protein subunits playing crucial role in the production and conversion of ATP, the body’s main chemical energy currency. On the other hand the actual sequence of one’s mitochondrial DNA in a particular tissue or cell… Continue reading MitoWheel 1.0: the human mitochondrial genome just got visual!
I found this quote in John Battelle’s blog from a recent CNET article on ex-Googlers by Stephanie Olsen, but I’d like to repeat it just with a different emphasis as I found all the other parts interesting for the biotech community except the one sentence bolded by Battelle. So I bolded those parts:
In my former blog post inF.A.Q. for 23andMe: what if I have mitochondrial DNA from Pa? I meditated on 23andMe‘s capability of detecting paternal mitochondrial DNA in their customers’ saliva with their Illumina microarray chips scanning around 2000 mitochondrial single nucleotide variants. Published here the initial answer of the 23andMe Editorial Team to this fairly… Continue reading 23andMe on the biparental inheritance of mitochondrial DNA and more
SciFoo is over, and I’ve just arrived back to New Orleans from SF. First of all: a big thanks for the organizers (Chris DiBona, Timo Hannay, Tim O’Reilly, Google, Nature, O’Reilly) and campers, it was really the highest end. Here is a quick SciFoo key terms summary (photos, detailed accounts later): “scientific data” One of… Continue reading SciFoo Camp, 2007: data (Google) publishing (Nature) geeks (O’Reilly)
23andMe is a biotech focused web startup based in Mountain View, California (yes, the Googleplex neighbourhood) self-defined as “an early stage startup developing tools and producing content to help people make sense of their genetic information. Our goal is to take advantage of new genotyping technologies and help consumers explore their genetics, informed by cutting… Continue reading 23andMe: the early bird of web based biotech startups
Check out Grailsearch.org, which was started at the end of January and is hosted by software engineer Jim Craig with a deep interest in aging and bioinformatics. Grailsearch is a “community web portal intended for use by biogerontologists, students of biogerontology, software engineers, biochemists or anyone else interested in working towards the search for systems… Continue reading Grailsearch.org: aging information from a systems biology perspective
Dear stem cell biologists and bioinformaticians: I’ve got a pretty serious question for you. How would you define and quantify the native (endogeneous, in-built) regenerative potential of a tissue/organ or more generally of a specially localized functional cell population in the human body? In the literature the term “regenerative potential” of a tissue is often… Continue reading How would you define the regenerative potential of a tissue/organ?
Check out the brand new BioMed Search, it is fantastic, currently over 1 million images have been indexed from peer-review journals in biomedical fields and more is on its way. BioMed Search has been created by Alex Ksikes, currently a Ph.D. candidate in Computer Science with focus in Computational Learning Theory at the University of… Continue reading The image of science: Google-like Biomedical Image Search Engine for pros
The first official issue of the new biological video protocol site JoVE or Journal of Visualized Experiments will be available today 11 pm EST, November 30, 2006. The graph shows November traffic in term of unique visitors, first 2.5 weeks mainly uploaders, authors, editors and editors’ friends used the page, from 17th there was a… Continue reading JoVE stats: blogosphere and Nature News traffic before official launch
John Cumbers made the Drosophila CHiP protocol video. He is a graduate student at the Tatar lab in Brown University, USA. Below are his answers to the blogterview questions and through answer 5 you can take a fresh look at the bottom-up approach of synthetic biology.
Briefly: A lot. As you might have noticed, for me as biotechnologist/life extensionist, the most important reference group is the group of IT people, because of the engineering approach, software-hardware tools, intuition concerning technology and funds. After Reason and Chris, our next answerer is Jim Craig, who published his answers here as a comment first… Continue reading The bioinformatics bet: what can IT folks do for life extension?