Biostar Beta. Not for public use.
45 results • Page 1 of 2
Once in a while I get the thrill of someone sending me a really good tip - that surge that comes with knowing that I know something that most people don't. That rush of knowing that soon I'll get to spill the beans. It's great, even if it upends my widely disseminated opinions. Even if a moment later I realize that if I had thought harder I would have unearthed the nugget on my own. All of which is the case here -- my tea leaf reading that Roche partnering with Illumina on diagnostics indicated that Genia is no more …
written 4 months by
Omics! Omics!
RNA-seq is a widely used approach to investigate gene expression and increasingly is used in time course studies to characterize transcriptomic changes over time. Two primary options are available as controls in time course experiments: samples collected at the first sampling time are used as controls (temporal control, TC) and samples collected in parallel at ...
written 4 months by
RNA-Seq Blog
I’m interested in how we bring medicines to patients faster and more accessibly. The technologies required are multifaceted. On the one hand, there’s discovery — for example, single-cell sequencing...
written 4 months by
RNA-Seq Blog
Principal component analysis (PCA) is an essential method for analyzing single-cell RNA-seq (scRNA-seq) datasets, but for large-scale scRNA-seq datasets, computation time is long and consumes large amounts of memory. Researchers from RIKEN Center for Biosystems Dynamics Research review the existing fast and memory-efficient PCA algorithms and implementations and evaluate their practical application to large-scale scRNA-seq ...
written 4 months by
RNA-Seq Blog
10X Genomics original product was a kit for generating linked reads from genomic DNA. The idea had been kicking around for a while, partitioning long DNA into compartments and generating tagged libraries from each compartment. This enabled both genome assembly and haplotyping from very small amounts of DNA. When first reviewing 10X's slides from J.P. Morgan I had this thought "where's the genome kits" but then forgot to include it in my write-up. Now I'm even more chagrined to discover that the explanation had been posted days before the conference: 10X has told their customers that their genome library kits …
written 4 months by
Omics! Omics!
The widespread establishment of statistics departments in the United States during the mid-20th century can be traced to a presentation by Harold Hotelling in the Berkeley Symposium on Mathematical Statistics and Probability in 1945. The symposium, organized by Berkeley statistician Jerzy Neyman, was the first of six such symposia that took place every five years, […]
written 4 months, 1 week by
Bits of DNA
Time to close out J.P. Morgan season with a grab bag of kvetches and kibbitzing on multiple 'omics companies that presented. Much of this has been stimulated by Twitter discussions, with particular credit going to Varro Analytics and Albert Vilella. While I've never been to J.P. Morgan physically and am skeptical I'll ever go, reviewing all this is a great prep for AGBT -- which I'm happy to be returning to this year for it's last Marco Island appearance for many years (forever?).Read more »
written 4 months, 1 week by
Omics! Omics!
Using k-mers and taxonomy to find contamination in metagenomes
written 4 months, 3 weeks by
Living in an Ivory Basement
Some things in Genbank look ...odd.
written 4 months, 3 weeks by
Living in an Ivory Basement
Algorithmic bias is a term used to describe situations where an algorithm systematically produces outcomes that are less favorable to individuals within a particular group, despite there being no relevant properties of individuals in that group that should lead to distinct outcomes from other groups . As “big data” approaches become increasingly popular for optimizing complex […]
written 6 months, 1 week by
Bits of DNA
Yesterday I found out via a comment on this blog that Yuval Peres, a person who has been accused by numerous students, trainees, and colleagues of sexual harassment, will be delivering a lecture today in the UC Davis Mathematical Physics and Probability Seminar. The facts I am aware of at least 11 allegations by women of […]
written 6 months, 2 weeks by
Bits of DNA
Also, for the developer types: they offer a way for you to interact with the Aquaria software to add your own features of interest with their API. Maybe you have new mutations you have found in some sequence you’ve obtained in your lab, for example. They are offering guidance on that here: http://bit.ly/aquaria-features. They touch on this […] The post OpenHelix to exhibit at TRICON appeared first on Open Helix.
written 7 months by
Open Helix
As often happens, last week’s tip on visualizing structures led me to some more reading and thinking about creating protein structures. And although it’s important for biologists to be able to use more of the information about protein structures and variations in their work from tools like Aquaria or PDB, it’s also important for some researchers to be on the […] The post VIDEO TIP OF THE WEEK: DESIGNING PROTEINS, USING ROSETTA appeared first on Open Helix.
written 7 months by
Open Helix
This week’s highlighted discussion tackles the topic of small projects for folks who are just beginning their training in bioinformatics, or possibly a career transition into a new area. It’s an issue that has come up a number of times, and this new idea for connecting students and projects is a good one, I think. […] The post WHAT’S THE ANSWER? (BEGINNER PROJECTS TO PICK UP) appeared first on Open Helix.
written 7 months by
Open Helix
It’s been 3 years since we last visited that old favourite recurring topic, data corruption by Excel. Specifically, the unwanted auto-conversion of identifiers that look like dates, e.g. SEPT1, to – well, dates. Here’s a new twist – well, a two year-old twist in fact, as I don’t keep up to date with this field … Continue reading When your tools are broken, just change the data
written 7 months, 2 weeks by
What You're Doing Is Rather Desperate
When Marlion Pickett runs onto the M.C.G for Richmond in the AFL Grand Final this Saturday, he’ll be only the sixth player in 124 finals to debut on the big day. The sole purpose of this blog post is to illustrate how incredibly easy it is to figure this out, thanks to the dplyr and … Continue reading Debuting in a VFL/AFL Grand Final is rare
The @sydstats Twitter account uses this code base, and data from the Transport for NSW Open Data API to publish insights into delays on the Sydney Trains network. Each tweet takes one of two forms and is consistently formatted, making it easy to parse and extract information. Here are a couple of examples with the … Continue reading Extracting Sydney transport data from Twitter
written 8 months, 2 weeks by
What You're Doing Is Rather Desperate
"A woman in Scotland can feel virtually no pain due to a mutation ...At age 65, the woman sought treatment for an issue with her hip, which turned out to involve severe joint degeneration despite her experiencing no pain. At age 66, she underwent surgery on her hand, which is normally very painful, and yet she reported no pain after the surgery. Her pain insensitivity was diagnosed by Dr Devjit Srivastava, Consultant in Anaesthesia and Pain Medicine at an NHS hospital in the north of Scotland and co-lead author of the paper....which the researchers have described for the first time …
written 1 year, 1 month by
Kevin's GATTACA World
Source: https://stackoverflow.com/questions/2709458/how-to-replace-spaces-in-file-names-using-a-bash-script#non-recursive methodfor f in *\ *; do mv "$f" "${f// /_}"; done
written 1 year, 1 month by
Kevin's GATTACA World
size:giganticin Windows Explorer to look for > 128 Mb sized files
written 1 year, 1 month by
Kevin's GATTACA World
I’m excited to be joining Ginkgo Bioworks. Ginkgo and the synthetic biology community have an incredible amount of useful data in intricate experimental designs, measured screening outcomes and pre-existing biological knowledge. I’ll help organize, present, compute on and do science with this data. I hope to enable downstream applications that improve agricultural sustainability and food security. I’m motivated to help with building an increasingly fair and climate friendly agricultural system due to the dire warnings about the state of our planet. There are many different ways to contribute on mitigating climate change, from personal action to politics to your daily …
written 1 year, 3 months by
Blue Collar Bioinformatics
This blog has moved to my new personal website and from now on can be found here: http://lexnederbragt.com/blog/. No new posts will be added from now on, but old posts will stay up.    
written 1 year, 5 months by
In between lines of code
The concept of pseudoalignment was first introduced in Nicolas Bray’s PhD Thesis and is one of the core concepts behind the fast RNA-Seq quantification in kallisto. A pseudoalignment of a read is simply a set of target sequences that the … Continue reading →
written 2 years, 3 months by
Bits of Bioinformatics
Earlier this year, I wrote a post about the new first-semester bachelor course “Introduction to Computational Modelling for the Biosciences” ​at our institute. A quick summary: from 2017, the Biosciences bachelor study program will incorporate Computing in Science Education (CSE) into the different subjects a new course “Introduction to Computational Modelling for the Biosciences” will […]
written 2 years, 5 months by
In between lines of code
Despite my current ranking of 15th in Biostar, myriad page views of my BAS™ post (albeit mostly misdirected perverts), and positive response for my celebrated campaign against more microarray papers, for some reason I was not "comped" an all-expenses paid trip as honorary blog journalist to this year's Advances in Biology and Genome Technology, which is kind of like CES for sequencing people, except AGBT is still worth attending. Normally the oversight would not bother me, as bioinformatics itself is not the focus of this meeting, but the flood of #AGBT tweets would not let me forget this fact and I was forced …
written 3 years by
Jermdemo
As part of the bachelor-studies reform here at the University of Oslo, the Institute of Biosciences, where I work, is reorganising its bachelor curriculum. One exciting part is the implementation of the Computing in Science Education (CSE) project, into the different subjects. The goal of the CSE project is to make calculations/computing an integral part […]
written 3 years, 2 months by
In between lines of code
The first ever RStudio conference was held January 11-14, 2017 in Orlando, FL. For anyone else like me who spends hours each working day staring into an RStudio session, the conference was truly excellent. The speaker lineup was diverse and covered lots of areas related to development in R, including the tidyverse, the RStudio IDE, Shiny, htmlwidgets, and authoring with RMarkdown. This is not a complete list by any means — with split sessions I could only go to half the talks at most. Here are some noncomprehensive notes and links to slides and resources for some of the awesome …
written 3 years, 3 months by
Getting Genetics Done
A while back I wrote this post about how I stay current in bioinformatics & genomics. That was nearly five years ago. A lot has changed since then. A few links are dead. Some of the blogs or Twitter accounts I mentioned have shifted focus or haven’t been updated in years (guilty as charged). The way we consume media has evolved — Google thought they could kill off RSS (long live RSS!), there are many new literature alert services, preprints have really taken off in this field, and many more scientists are engaging via social media than before.People still frequently …
written 3 years, 3 months by
Getting Genetics Done
This is my notebook for creating a custom engine in GATK. Description I want to read a VCF file and to get a table of category/count. Something like this: HAVE_ID TYPE COUNT YES SNP 123 NO SNP 3 NO INDEL 13 Class Category I create a class Category describing each row in the table. It's just a List of Strings static class Category implements Comparable {
written 3 years, 4 months by
YOKOFAKUN
45 results • Page 1 of 2

Planet Feeds

Omics! Omics!
A computational biologist's personal views on new technologies & publications on genomics & proteomics and their impact on drug discovery
3 posts - last updated 4 months ago
RNA-Seq Blog
Transcriptome Research & Industry News
3 posts - last updated 4 months ago
Bits of DNA
Reviews and commentary on computational biology by Lior Pachter
3 posts - last updated 4 months, 1 week ago
Living in an Ivory Basement
3 posts - last updated 4 months, 3 weeks ago
Open Helix
Learn to use Bioinformatics Resources
3 posts - last updated 7 months ago
What You're Doing Is Rather Desperate
Notes from the life of a [data] scientist
3 posts - last updated 7 months, 2 weeks ago
Kevin's GATTACA World
My Weblog on Bioinformatics, Genome Science and Next Generation Sequencing
3 posts - last updated 1 year, 1 month ago
Blue Collar Bioinformatics
Community built tools for biological data analysis
2 posts - last updated 1 year, 3 months ago
In between lines of code
Biology, sequencing, bioinformatics and more
3 posts - last updated 1 year, 5 months ago
Bits of Bioinformatics
3 posts - last updated 2 years, 3 months ago
Jermdemo
Mostly bioinformatics, NGS, and cat litter box reviews
3 posts - last updated 3 years ago
Getting Genetics Done
Getting Things Done in Genetics & Bioinformatics Research
3 posts - last updated 3 years, 3 months ago
YOKOFAKUN
3 posts - last updated 3 years, 4 months ago
Ewan's Blog: Bioinformatician at large
3 posts - last updated 3 years, 5 months ago
opiniomics – has moved! www.opiniomics.org
opiniomics - has moved! www.opiniomics.org
1 post - last updated 4 years, 4 months ago
Genomes Unzipped
A group blog providing expert, independent commentary on the personal genomics industry.
3 posts - last updated 5 years, 6 months ago
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