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nue reading hadoop 101 for bioinformaticians 1 hour crash course code and slides bioinformatics hadoop mapreduce crowdsourcing google s new mission statement newgooglemissionstatement november 3 2014 november 3 2014 posted in partial immortalization larry page acknowledges in a recent interview that the google s mission statement is outdated and became irritatingly narrow google mission statement changing the game absolute protein quantification by relating histone mass spec signals to dna amounts and cell numbers september 17 2014 september 17 2014 posted in bioinformatics biology proteomics quantification 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 pleasingly parallel mcmc cracked wide open for mapreduce and hadoop march 9 2014 february 14 2015 posted in partial immortalization mcmc methods guarantee an accurate enough result say parameter estimation for a phylogenetic tree but they give it to you usually in the long run and many burn in steps might be necessary before performing ok and if the data size grows larger the number of operations to draw a sample grows larger too n o n continue reading pleasingly parallel mcmc cracked wide open for mapreduce and hadoop bioinformatics computer science hadoop mapreduce markov chain monte carlo mcmc 2 recent global alliance for genomics and health standard candidates adam and google genomics march 3 2014 march 6 2014 posted in partial immortalization global alliance for genomics and health includes 150 health and research organizations to progress accelerate secure and responsible sharing of genomic and clinical data ga4gh for short is something you will here about more and more in the short term future in the context of genomics standards think of mainly data formats and code to access and process continue reading 2 recent global alliance for genomics and health standard candidates adam and google genomics genomics global alliance for genomics and health google standards 3 recent hadoop mapreduce applications in the life sciences rna structure prediction neuroimaging genetics eeg signal analysis february 26 2014 february 26 2014 posted in partial immortalization 3 open access papers 3 prototypes source code available only for 1 healthy diversification of topics 1 enhancement of accuracy and efficiency for rna secondary structure prediction by sequence segmentation and mapreduce code available haven t found it referenced in the paper our previous research shows that cutting long sequences into shorter chunks predicting secondary structures of continue reading 3 recent hadoop mapreduce applications in the life sciences rna structure prediction neuroimaging genetics eeg signal analysis biology clinical data hadoop life sciences mapreduce google invests into dnanexus aging driven big data bioinformatics without the hadoop ecosystem january 3 2014 january 4 2014 posted in calico genomics google partial immortalization first time dnanexus made me think a little about what they can achieve was when they came up with an alternative search and browse interface for the complete sequence read archive sra database they came to the rescue as ncbi discontinued sra in 2011 although later they ve changed their mind so sra is still up and running there continue reading google invests into dnanexus aging driven big data bioinformatics without the hadoop ecosystem calico dnanexus genomics google hadoop mapreduce proteomics coming of age for proteogenomics 10 less human protein coding genes based on mass spec proteomics data december 30 2013 posted in partial immortalization guessing the number of real protein coding genes is an ancient bioinformatics game and now a new argument newish research field has been applied to this problem proteogenomics can refer to different type of studies but the basic idea is that mass spectrometry peptide protein evidences are used to improve genome annotations now a joint spanish continue reading coming of age for proteogenomics 10 less human protein coding genes based on mass spec proteomics data genomics human mass spectrometry protein coding genes proteogenomics proteomics three links in aging regenerative medicine healthy lifespan extension 17 december 2013 december 17 2013 posted in aging bioinformatics biology calico cancer epigenetics life extension partial immortalization 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 three links in aging regenerative medicine healthy lifespan extension 8 december 2013 december 7 2013 december 7 2013 posted in aging biology fda life extension 1 is aging linear or does it follow a step function a good simple question on quora that surprised even aubrey de grey if you are a bioinformatician out there looking for a new pet project go pull together some data try to plot it let me know if you have something continue reading three links in aging regenerative medicine healthy lifespan extension 8 december 2013 calico three links in aging regenerative medicine healthy lifespan extension 24 november 2013 november 24 2013 posted in partial immortalization introducing a new post format by reutilising nat torkington s four short links format over at o reilly radar thanks nat 1 the hallmarks of aging good review by european scientists trying to put some pieces next to each other but not necessarily together the 9 hallmarks are genomic instability telomere attrition epigenetic alterations loss of proteostasis continue reading three links in aging regenerative medicine healthy lifespan extension 24 november 2013 aging lifspan extension regenerative medicine stem cells how to build a colorful life around life extension using different skills a personal story october 9 2013 october 9 2013 posted in aging career life extension partial immortalization personal here s an edited version of my quora answer to the question life decisions how do people who are talented in many areas decide what to do with their lives let me provide a personal story illuminating one option ruchira is talking about pick a complex challenge that you are passionate about that will require many different continue reading how to build a colorful life around life extension using different skills a personal story lavaamp cheapest pocket pcr thermocycler dreamed for diy biologists october 31 2009 october 31 2009 posted in biodiy biohacking biology biotechnology diy dna geek open science sci foo science science hacks scifoo 108 comments the lavaamp is a portable pcr thermocycler that has the potential to become the default garage biology home biology biodiy diybio tool once it hits the market think of apple ii for personal computing or makerbot for 3d printing the 1st lavaamp prototype was shipped this week from biodesic to gahaga biosciences and the process continue reading lavaamp cheapest pocket pcr thermocycler dreamed for diy biologists aging centric genetic health database in california 100k people 65yrs 700k snps telomeres too october 21 2009 october 21 2009 posted in aging california genetics genomics science usa 15 comments kaiser permanente alongside with ucsf plans for genetic analyses of an unprecedented 100 000 older californians the technology review writes in massive gene database planned in california the effort will make use of existing saliva samples taken from california patients whose average age is 65 their dna will be analyzed for 700 000 genetic variations called single nucleotide continue reading aging centric genetic health database in california 100k people 65yrs 700k snps telomeres too sage bionetworks update building an oa standard for human disease biology october 8 2009 october 8 2009 posted in bioinformatics biology science usa 18 comments 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 sage the nobel prize in physiology or medicine 2009 telomere telomerase blackburn greider szostak october 5 2009 october 5 2009 posted in aging cancer cell biology science marketing 16 comments for the discovery of how chromosomes are protected by telomeres and the enzyme telomerase press release the award goes to elizabeth h blackburn carol w greider and jack w szostak the problem of telomere telomerases is highlighting the double but strictly related aging cancer problem space blackburn lab greider lab szostak lab top 10 plos articles based on online usage september 16 2009 posted in open access science 17 comments big news at plos today mark patterson announced on the plos blog that as part of our ongoing article level metrics program we re delighted to announce that all seven plos journals will now provide online usage data for published articles i downloaded the entire dataset and as a starter sorted it according to combined usage continue reading top 10 plos articles based on online usage plos mapping neurons without glial cells snp genotyping w o whole sequencing may 3 2009 may 4 2009 posted in biology genomics nature neural personalized genomics science 10 comments nature s journal club column is usually a good always a short read providing exciting angles on scientific topics papers from good researchers recently neuroscientist dave featherstone argued for a broader approach to brain mapping by not restricting it only to the connectome between neurons neurons are making up less than 10 of the human brain continue reading mapping neurons without glial cells snp genotyping w o whole sequencing visualize 23andme haplogroup defining snps with mitowheel april 7 2009 april 8 2009 posted in 23andme genetics genomics mitochondria mitowheel personalized genetics personalized genomics 33 comments last friday 23andme came up with haplogroup tree mutation mapper which is the first experimental feature that can be instantly tested by biogeek customers a large portion of the company s customer base in its freshly launched technology sandbox 23andme labs that is much like google labs haplogroup tree mutation mapper shows you which particular mutations continue reading visualize 23andme haplogroup defining snps with mitowheel bright cells big city cellular images hit broadway march 10 2009 march 10 2009 posted in biology image innovation new york photo science animation science marketing usa 6 comments surprise email from conor mckechnie ge healthcare proving the aesthetics of science and the value of blogging a while back you posted an inspiring piece linking to harvard s biovisions inner life of the cell it was 2006 it got me thinking that we could do something similarly inspiring with actual cellular images entered into continue reading bright cells big city cellular images hit broadway why the dyna vision g1 android telemedicine app can only be used by licensed physicians march 3 2009 march 3 2009 posted in biodiy diy future gadget geek medicine regulation technology 14 comments let us assume that you are a technological early adopter a maker a hacker a geek your software hardware skills and experiences are much better than the bulk of licensed physicians you also have a g1 now imagine a mobile application gadget in a belt pouch that is the most advanced telemedicine solution in the market with this application gadget you were continue reading why the dyna vision g1 android telemedicine app can only be used by licensed physicians android many eyes visualizations fda application approvals 2000 2008 february 28 2009 february 28 2009 posted in biotechnology fda industry us usa 16 comments take a look at the fda application approvals 2000 2008 visualization created by user mktlgcs over at ibm s many eyes to get an aerial view on the us pharmaceutical industry google health ibm real time vital medical data stream february 5 2009 february 5 2009 posted in partial immortalization 12 comments forbes article letting google take your pulse via mattcutts on thursday google and ibm will unveil a new initiative that will allow google health a site where users can store and track information about their medical history to connect to and stream data from medical devices in demonstrations ibm and google fitted wi fi radios to continue reading google health ibm real time vital medical data stream sciencex2 is dead long live signtific february 1 2009 posted in science silicon valley technology the institue for the future usa x2 4 comments the folks at the institute for the future have been busy lately and as a result signtific has been launched replacing sciencex2 check this the about and faq pages if it s new to you or just simply explore practical dna hugh rienhoff s got a story to tell january 29 2009 posted in biodiy biohacking biology diy genetics genomics medicine science hacks 8 comments after the nature cover article hugh rienhoff and the story of my daughter s dna is now covered by wired magazine i wrote about hugh a fellow scifoo camper as an example of any future biodiy effort in the conditions of a mass biotech diy movement and now the wired piece gives us more context and details continue reading practical dna hugh rienhoff s got a story to tell bioblocks outsourcing biotech one block at a time january 15 2009 january 15 2009 posted in biotechnology industry innovation 15 comments friend dan erlanson co editor in chief of the niche and smart fragment based drug design blog practical fragments sent me this story on the recession proof business model of a biotech company called bioblocks and his founder medical chemist peter pallai approximately one out of 5 000 compounds pass an initial screen hit the designated biological target continue reading bioblocks outsourcing biotech one block at a time 1st uk maker faire newcastle march 2009 makers wanted december 16 2008 posted in biodiy diy geek make open science open source science science hacks technology uk 7 comments the first euro maker faire in brussels was an evenin...