Join us
@fulcrumgenomics
!
Nowhere else can you have access to so many diverse and challenging
#Bioinformatics
and
#Engineering
problems across so many clients and domains:
‣ 10+ 5 year clients
‣ 100+ projects completed
‣ 50+ clients served
We're hiring
@fulcrumgenomics
! We're looking for an experienced bioinformatician to join our team and work on exciting projects in technology development and biomedical research. If you're interested in becoming part of our team, drop us a line here:
Experienced Bioinformaticians:
Comment below the one thing you'd like to tell junior Bioinformaticians.
New Bioinformaticians:
Read below for an awesome list of career tips.
In response to this unoriginal tweet, I’ll go first:
Never trust your first results, especially when they agree with what you expected. Skepticism is the price we pay for amazing science.
I am proud to announce the launch of ExcelBio!
Driven by overwhelming demand from Biologists: build, manage, and execute your
#Bioinformatic
workflows all from your favorite GUI, Excel. We are proud to support Illumina SampleSheets as our first product. DM me for a demo!
#Bioinformatics
software lifecycle:
Someone has written this before.
All of them are unsupported, and I don’t want to pay for it.
Fine, I’ll write my own, I can do a better job anyhow.
Job’s done, but no money for maintenance or support.
We now have N+1 BFX software.
#Bioinformatics
on AWS has never been easier!
So long CloudFormation; say hello to the
#AWS
Genomics CLI. I've used it with snakemake, nextflow, cromwell, and miniwdl. It takes the pain of going from a working workflow locally to one on the cloud: 🧑🍳💋.
I have a confession to make...
I have replaced writing bash scripts with
#Snakemake
for all my
#Bioinformatics
analyses, even trivial ones...
I'll let you figure out why.
Excited to share a new preprint with
@XiChenUoM
and
@lpachter
introducing seqspec for describing, organizing, and annotating elements in sequencing libraries. seqspec is a machine readable specification + an associated suite of tools. 1/9
@sebatlab
Great folks coming out of undergrad are getting six figure
#Bioinformatics
jobs, let alone out of a PhD or post doc. They both need A TON of training, but they’re worth it. Whether or not you like it, you’re competing with us.
Breaking: CDC says fully-vaccinated people can go back to using TopHat again, with all custom scripts written in PERL and committed to CVS (not the pharmacy).
#Bioinformatics
By the age of 30, you should have uninstalled/reinstalled conda 5 times with over 100 PERL scripts saved that you don't have any plan to actually use.
#Bioinformatics
Dear academics, I'm going to eventually read your code. Please feel the appropriate amount of shame from the start about your hard-coded paths, missing required files, and major assumptions about file naming. Your frenemy, industry.
I love writing
#Bioinformatics
tools, plumbing them into pipelines, written with care, and seeing them produce novel Biological insights at scale.
If that’s you, come join us
@fulcrumgenomics
Sometimes I wonder if people even use Picard tools in
#Bioinformatics
Time to get a bit personal about how most of my tools “never made it”, imposter syndrome, and it’s ok to fail.
A thread 1/n
It’s just lab work. Can’t you just sequence each chromosomes individually? Data ready tomorrow right?
Translating how some Lab Scientists talk about
#Bioinformatics
. What’s your experience?
Some of the things I’ve worked over the past year:
> cancer vaccines
> genome editing
> novel DNA sequencers
> single cell-finding algos
> clinical diagnostics
> forensics genealogy
> modified oligonucleotides
> open source software
> high performance file systems
> file formats
We’re seeing organic adoption of
@LatchBio
by more than a few of our clients. Here’s why we are very positive on the platform (hint: Biologists running Snakemake), our excellent experiences working with the Latch team despite past public behavior, and overall thoughts. Thread…
I am proud to announce the launch of ExcelBio!
Driven by overwhelming demand from Biologists: build, manage, and execute your
#Bioinformatic
workflows all from your favorite GUI, Excel. We are proud to support Illumina SampleSheets as our first product. DM me for a demo!
New details on the
@PacBio
SBB short read sequencing platform presented by Jonas Korlach at
@agbt
, including a video demo of the instrument. This is a big moment for
@PacBio
!
Trying to recruit the best Bioinformaticians over here.
Fair and equitable pay, great life-work balance, engaging and challenging problems, world class clients and
#Bioinformatics
team.
I have only but one problem to solve…
grep, but for FASTQS, but now more grep-like
We've done a lot of work
@fulcrumgenomics
to try emulate grep, but for FASTQs. Almost all of the grep command line arguments are now implemented.
Try it out and submit your bug reports.
#Bioinformatics
grep, but for FASTQs
I’m looking for folks to try out a major upgrade to fqgrep that makes the usage almost the same as vanilla grep.
Please build off of this branch while I add unit tests:
We in
#Bioinformatics
need to write unit tests.
I almost always ready tests first. They are the best documentation for how the author intended for the code to be used and behave.
Write at least a few to help me on my way.
Tip: Starting code reviews by looking at tests is a good way to get a sense of what the change is about (it'll reveal things often hard to spot in the change itself). If there are no tests, stop reviewing and ask for tests.
Exciting news from
@Verilylifesci
on this $1Bn funding to further our precision health impact, including evidence generation. Big congrats to
@stephengillett
, who will be our new CEO, and deep gratitude to Andy Conrad. We're set up for great things ahead!
Building a
#BioInformatics
tool repository to me feels like the same as annotation and curation for variant databases:
1. garbage in, garbage out
2. everything is done manually
3. relying on academic grade tools (data sources) is fraught with peril
I'm seeing wide-spread layoffs in
#Bioinformatics
and
#biotech
.
So many good and talented people affected; I'm here to listen and help in my own small way.
For all the excitement of
#Bioinformatics
software in new programming languages, the API designs and the ease of use for other developers are… not good. That’s why I sometimes call it academic grade. Gets the paper published, but helps no one later.
Come work with us
@fulcrumgenomics
!
Bioinformaticians and Computational Biologists welcome!
We solve interesting biological problems through engineering and bioinformatics for a diverse set of clients. We also value life outside of work. See more below.
#Bioinformatics
1/n
Wow, what an
#ESHG2022
talk!
#CRISPR
-Cas9 causes off target structural variants in zebrafish
NOT detected by short-read sequencing and ARE passed on to offspring.
Huge implications to studies and any possible future therapeutic editing
Paper is here:
I don’t work with bullies.
I was bullied as a kid, and now I have the privilege to choose with whom I work. I don’t need you, you need me. Thank you next.
Why don’t journals have a read only GitHub organization that authors must deposit code (and small datasets) into? I’ve been burned by folks moving, deleting, or overwriting.
Same for wet-lab protocols not described in the paper or supplementary materials.
Isn’t this par for the course
#RStats
? R is a programming language that actively fights software engineering best practices. Extra points if you can actually reproduce the environment and not have hard coded paths.
I want IGV for complex rearrangements, to visualize long reads aligned in graph (not a dag) form against many short contigs (non-linear reference) or distant segments (linear reference). Imagine a SAM file with many complex non-linear chimeric alignments. This must exist.
#fgbio
2.0, the second major release, is now available.
A major theme of this release is performance of the UMI-related tools. And for those using picard's MergeBamAlignment, try using fgbio ZipperBams instead. Same author, new tool.
#Bioinformatics
There are so many intangible benefits supporting users of your open source
#Bioinformatics
, but at some point you have to get paid for it. The folks asking the questions are getting paid, so why not us?
@bernhardsson
Most bioinformatic tools are command line based, have wildly different compute resource requirements, are data/file heavy, and are insidious to install/containerize. Airflow, Luigi, and others are not built with those things in mind. And so we have our own.
SnakeLatch?
I am genuinely excited at the prospect of a
#Bioinformatics
platform that has an amazing UI for Biologists on which Bioinformaticians can develop using Snakemake.
How does one leverage a genetic database of millions of samples to solve cold cases or identify human remains? To find even 4th degree relatives with only 10K SNPs?
#Bioinformatics
#Forensics
A 🧵…
My new aligner is awesome.
It’s not meant to be fast, but instead gets to single molecule base-pair resolution of some very interesting events. I can’t say what yet, since no one is going to see it for a while, but it’s awesome. I just need to tell people.
Will there ever be good digital infrastructure in biotech? Alternate title: "Part of the reason it's hard to hire developers in bio is because they don't have the tools to succeed that they do elsewhere - will that ever change?"
How to differentiate yourself in
#Bioinformatics
and
#CompBio
:
Learn a “performant” language in addition to “data science” languages.
Former: eg. Rust, C/C++, JVM
Latter: eg. Python, R, PERL
@dgmacarthur
Heng is exceptional at many things, but one thing that is rarely talked about. He skates to where the puck will be. And has a toolkit ready for when the data arrives.
Join us
@fulcrumgenomics
!
Nowhere else can you have access to so many diverse and challenging
#Bioinformatics
and
#Engineering
problems across so many clients and domains:
‣ 10+ 5 year clients
‣ 100+ projects completed
‣ 50+ clients served
grep, but for FASTQs
I’m looking for folks to try out a major upgrade to fqgrep that makes the usage almost the same as vanilla grep.
Please build off of this branch while I add unit tests:
Academics want me to peer review and don’t want to compensate me for it?
It’s supplanting actual client work where I’m getting paid: your lack of budgeting is not my emergency.
And also, perhaps if you paid reviewers you’d actually get some.
🎵🎵🎵 Don’t be fooled by the socks that I got,
I’m still, I’m still the Bioinformatician on the block.
I used to have short reads, now they’re long.
No matter what I sequence, I know where they map to.🎵🎵🎵
(Thank you
@PacBio
for the socks!)
Want a feature request in a open source
#Bioinformatics
software? Sponsor it!
So many of our
#Bioinformatics
tools and features have come about through industry sponsorship and giving back (we love it).
But…
Infinity also enables 10x greater throughput with 90% less
#DNA
input than legacy long reads. We anticipate an early access launch for Infinity technology in the second half of the year.
Introducing G4, the world’s most powerful benchtop sequencing platform. Built with novel high-performance chemistry and advanced engineering to deliver accuracy, speed and flexibility, G4 has the ability to power a wide range of
#genomic
applications.
Join us
@fulcrumgenomics
!
Nowhere else can you have access to so many diverse and challenging
#Bioinformatics
and
#Engineering
problems across so many clients and domains:
‣ 10+ 5 year clients
‣ 100+ projects completed
‣ 50+ clients served
Validate your VCFs before you publish them.
GIAB/NIST and Platinum Genomes VCFs don’t strictly follow the spec.
I’m writing my own tool because I’m a masochist. Early testers are appreciated as I add more features and squash bugs.
#Bioinformatics
There are a lot of positive outcomes in the above process. Folks learn by doing, the software was written to solve an immediate problem, a diversity of ideas and solutions…
But let’s not pretend there isn’t a Bioinformatics SW graveyard, and a lot of it comes down to money.