439 results • Page 1 of 15
The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed... go to blog
The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed... go to blog
I proposed last year that there should be a regular racing event for human genomics. The only real competitor in is this interesting race seems to be Steven Kingsmore's group at Rady Children's Hospital. I was sent an embargoed press release from Illumina about a new record by that group, which clocks in at 13.5 hours from patient sample to clinical report. A New England Journal of Medicine paper (hence the embargo, ending just before I post this) reports on … go to blog
The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed... go to blog
Yesterday was Matt Meselson's 91st birthday. I have only met him a few times and he wouldn't know me from Adam, but he is a particularly interesting individual I've had the good fortune to converse with. I'm putting out a plea now for a skilled biographer to write his life, because it certainly has been an interesting and impactful one, with scientific work stretching from the early beginnings of molecular genetics to a preprint just recently posted on BioRxiv.Read more … go to blog
The title really says it -- London Calling has actually already begun and here I am pretending to write a "before the conference" piece. Of course, since everything is virtual again this year I can actually do this since I haven't watched anything yet nor have seen any tweets -- and the big technology announcement section isn't for a few hours so I have loads of time to write! Sadly, nor have I gone and looked at what I've written … go to blog
Leonardo Martins tweeted that xz can compress a 1.4 million SARS-CoV-2 genomes in a 39GB FASTA down to 74MB. That is a very impressive compression ratio! This reminds me of my earlier work on FM-index construction. For an experiment, I downloaded ~400k SARS-CoV-2 genomes from EBI’s COVID-19 data portal (GISAID has ~1.5M genomes but imposes restrictions) and generated an FM-index of these sequences in both strands with ropebwt2 ropebwt2 -do sars-cov-2.fmd sequences_fasta_2021-05-15.fa.gz The command line took ~30 minutes. The output … go to blog
This command allows you to see what apps are consuming internet. ss -p go to blog
A painting hangs in the Nijmegen Town Hall showing a young woman with an old man lying in her lap, and six sons standing next to her: two in red, two in green, and two in white. It is accompanied by the following text:The wife of the old man says:“Remark and see that I declareThe two in red are my father’s brothers.The two in green are my mother’s brothers.The two in white are my childrenand I, the mother, am married … go to blog
The GISAID database has been the workhorse for storing and distributing SARS-CoV-2 sequences during the COVID-19 pandemic and recently passed one million entries. There was some Twitter chatter wondering about the hardware breakdown for this, as it isn't really easy to get out of GISAID. I had done a somewhat arduous partial take at this for my VIB talk last month, but in the meantime GISAID had granted me some additional access to metadata which I've been too busy to … go to blog
Concepts in phased assembly: Contig: a contiguous sequence in an assembly. A contig does not contain long stretches of unknown sequences (aka assembly gaps). Scaffold: a sequence consists of one or multiple contigs connected by assembly gaps of typically inexact sizes. A scaffold is also called a supercontig, though this terminology is rarely used nowadays. Haplotig: a contig that comes from the same haplotype. In an unphased assembly, a contig may join alleles from different parental haplotypes in a diploid … go to blog
If you haven’t heard about Clubhouse yet… well, it’s the latest Silicon Valley unicorn, and the popular new chat hole for thought leaders. I heard about it for the first time a few months ago, and was kindly offered an invitation (Club house is invitation only!) so I could explore what it is all about. […] go to blog
Our new editorial on equity, diversity, and inclusion in data science is out in BioData Mining. go to blog
It seems like this discussion comes up a lot. Choosing a differential expression (DE) tool could change the results and conclusions of studies. How much depends on the strength of the data. Indeed this has been coveres by others already (here, here).In this post I will compare these tools for a particular dataset that highlights the different ways these algorithms perform. So you can try it out at home, I've uploaded the code for this to GitHub here. To get … go to blog
Theophilus Painter (1889–1969) joined the faculty at the University of Texas in 1916 and except for a military stint during World War I stayed there his whole career. He was, in succession, instructor, associate professor, professor, distinguished professor, acting president (1944–1946), and president (1946–1952) of the University of Texas.These days, he is remembered for three things (1) erroneously claiming that humans possess 48 chromosomes—an error that plagued human cytogenetics for 33 years, (2) his willingness to curry favor with corrupt … go to blog
COVID-19 was and remains a major crisis in many countries, disrupting general life as well as scientific research. But how has it impacted scientific output in genomics?To evaluate this I investigated the number of papers published in PubMed Central (PMC) in the period from 2016 through 2020. I used total number of papers as well as those matching the genomics search term with the approach below:(genom*[Abstract]) AND ("2020"[Publication Date] : "2020"[Publication Date]) Here are the number of papers and genomics … go to blog
Romano JD, Moore JH. Ten simple rules for writing a paper about scientific software. PLoS Comput Biol. 2020 Nov 12;16(11):e1008390. doi: 10.1371/journal.pcbi.1008390. PMID: 33180774; PMCID: PMC7660560. [PubMed] [PLoS Comp Bio]AbstractPapers describing software are an important part of computational fields of scientific research. These "software papers" are unique in a number of ways, and they require special consideration to improve their impact on the scientific community and their efficacy at conveying important information. Here, we discuss 10 specific rules for writing … go to blog
I get asked a lot about the best ways to store sequence data because the files are massive and researchers have various levels of knowledge of the hardware and software. Here I'll run through some best practices for genomics research data management based on my 10 years of experience in the space.1. Always work on servers, not remote machines or laptopsOn-prem machines and cloud servers are preferred because you can log into the from anywhere using ssh or other protocol. … go to blog
Ian Holmes has a twitter poll right now on the use of “SNP” (single-nucleotide polymorphism) versus “SNV” (single-nucleotide variant). I have been bugged by the two terminologies for years, so I decided to write a blog post on it. Personally, I use “SNP” for germline events and “SNV” for somatic events, but I understand others think differently. Here are my thoughts. The wiki page for SNP defines a SNP as a nucleotide change “that is present in a sufficiently large … go to blog
It’s been a while. I hope you are all well. Shall we make some charts? About this time last year, one of my life-long dreams came true when I was told that I could work from home indefinitely. One effect of this – I won’t say downside – is that I don’t get through as … Continue reading Florence Nightingale’s “rose charts” (and others) in ggplot2 go to blog
This software company did something that I didn't expect... putting the variant calling on the phone itself .. "The variant calling is run directly on the phone, extracting the data from the file on your phone, processed on the phone, and only at the end the VCF file could be shared in the cloud for annotation and reporting by an accredited physician," Ascari said. The physician is necessary to assure that the result is of "diagnostic quality," he added.I honestly … go to blog
More spatial profiling news coming in from AGBT -- Harvard spin-out VizGen is launching in the U.S. an instrument implementing MERFISH technology. This sub-$300K instrument will initially enable panels of up to 500 genes to be profiled, with plans to expand that capacity to 1000. Users either pick from a menu of pre-designed panels or select genes using a Gene Panel Design Tool and VizGen would proceed to manufacturing the panel in around two weeks. VizGen CEO Terry Lo and … go to blog
Rant is ON! I've been having an utterly miserable experience with the LabRoots conference software that AGBT is using for their virtual meeting. This year has exposed many of us to a wide variety of teleconference and virtual meeting software and many of the glitches are small and hard to pin down. Or matters of personal preference (though if you don't share mine, you are simply wrong!). But now on two major platforms I've come across major issues with LabRootsRead … go to blog
My prediction that spatial would be a hot topic at AGBT was easy to make knowing I was sitting on embargoed news in the spatial space. This morning Rebus Biosystems announced the launch of the Rebus Esper system for wide field spatial profiling of gene panels with subcellular resolution. Rebus is promising that this instrument will offer true walkaway automation from fluidics through imaging, and data processing, requiring only one hour of hands-on time.Read more » go to blog
This year marks the 20th anniversary of the publication of the human genome reference sequence. As I enjoy recounting to people outside of the genomics field, the investment required to complete that initial assembly is staggering: ten years, dozens of laboratories, hundreds of sequencing instruments, and a billion dollars. Today, using the latest next-generation sequencing, […] The post Genome Reference: Moving to Build 38 appeared first on KidsGenomics. go to blog
Getting some miscellanea out before AGBT21 starts later this morningRead more » go to blog
439 results • Page 1 of 15
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