Thank you OBF (and especially Taz) for this lovely post about the GigaScience team. I've been going to your #BOSC meetings since 2011 and will miss catching up with you all each summer, but hopefully it's not goodbye!
01.10.2025 08:48 β π 7 π 2 π¬ 0 π 0
Thank you @openbio.bsky.social for summarizing a great (but too short) #OpenScience #OpenAccess story β¦ All of us lost a great team of friends and colleagues in this sad story.
01.10.2025 12:40 β π 4 π 0 π¬ 0 π 0
Scott Edmunds cuts the cake at the 2025 GigaScience birthday party at ISMB/ECCB 2025
An open letter about the recent cuts at GigaScience: www.open-bio.org/2025/09/30/2...
(open for signatures until the end of October)
#OpenScience #OpenData #GigaScience
30.09.2025 21:02 β π 8 π 12 π¬ 1 π 3
These are all valuable suggestions for handling the (sudden) end of a project.
Keep in mind that code which is not actively being used and maintained is dead and will quickly become useless.
Also few projects will be adopted by an active open source community.
29.09.2025 20:43 β π 3 π 1 π¬ 0 π 0
Ten simple rules for writing a PLOS Computational Biology quick tips article
If this had been in PLOS CB, it would have been a Ten Simple Rules (TSR) paper, not a Quick Tips (QT) paper. As we write in our TSR about writing a QT paper (in Rule 1): "Ten Simple Rules are more to develop soft skills, career promotion/advancement ..." π§ͺπ
β¬οΈ
journals.plos.org/ploscompbiol...
29.09.2025 20:23 β π 1 π 0 π¬ 0 π 0
π’ NEW GENOME ALERT
In #G3journal, Frandsen et al. present a chromosome-scale assembly of the tetraploid epazote, a perennial plant growing in tropical climates in the Americas with regional culinary and medicinal importance. buff.ly/Vbp0rde
26.09.2025 20:01 β π 4 π 4 π¬ 0 π 0
π§° Now published in Bioinformatics Advances: "Atlantool: A command line tool to retrieve DNA and RNA sequencing reads from BAM files by the read identifier"Β Β
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf226Β
Authors include: @nibor.org, @egiannoulatou.bsky.social
26.09.2025 09:02 β π 4 π 2 π¬ 1 π 1
A review on Gene Ontology evaluations
Abstract. The analysis of the large and heterogeneous datasets that characterize modern biology demands systems capable of representing biological knowledg
From @borja-pitarch.bsky.social and colleagues in #OUP 's #DATABASE journal | A review on #GeneOntology evaluations | #Bioinformatics #Genomics #Review #OpenScience #GO 𧬠π₯οΈ π§ͺ ππͺπΈ
β¬οΈ
academic.oup.com/database/art...
26.09.2025 13:07 β π 9 π 1 π¬ 0 π 0
Newly expanded version of my guide to scientific writing -- known as the β15 stepsβ -- published in PLOS Computational Biology. Special thanks to Γric Marty for creating a fantastic visualization.
Check it out: journals.plos.org/ploscompbiol...
#ScientificWriting #PLOSComputationalBiology
24.09.2025 17:54 β π 36 π 21 π¬ 1 π 2
How to write a scientific paper in fifteen steps
From @jdrakephd.bsky.social & @bahanbug.bsky.social in @plos.org #Computational #Biology | How to write a scientific paper in fifteen steps | #Education #Science π§ͺ πΒ #GoodReadingForAll CC/ @ppalagi.bsky.social
β¬οΈ
journals.plos.org/ploscompbiol...
25.09.2025 12:29 β π 9 π 6 π¬ 0 π 0
Important for #autistic people and other marginalized groups who are being targeted using health systems databases (particularly those on medicaid and medicare in the U.S.).
There is an ethical responsibility to stop targeting and de-identifying data is one of the best ways to help all of us.
24.09.2025 17:28 β π 4 π 1 π¬ 0 π 0
Ten simple rules for building and maintaining sustainable high-performance computing infrastructure for research in resource-limited settings
From @plos.org #Computational #Biology | Ten simple rules for building and maintaining sustainable high-performance computing infrastructure for research in resource-limited settings | #Africa #HPC #PLOSCBTSR π₯οΈ π§ͺ π
β¬οΈ
journals.plos.org/ploscompbiol...
23.09.2025 12:19 β π 4 π 4 π¬ 0 π 0
9 more days β¦ #Africa #Bioinformatics #Health #Informatics #Education
21.09.2025 21:28 β π 2 π 3 π¬ 0 π 0
βFrom Data to Discovery: Opportunities with the African Bioinformatics Instituteβ delivered at the recent Data for Health in Africa Meeting & 5th DS-I Africa Consortium Meeting in Accra, Ghana. Explore ABIβs vision as well current and future activities: www.linkedin.com/pulse/showca...
11.09.2025 06:21 β π 2 π 1 π¬ 0 π 0
Validate User
From #NAR journal | #Cancer #histone mutations impact protein binding and DNA repair with possible links to genomic instability | From my friend @davidlandsman.bsky.social & former colleague @panchenko-lab.bsky.social | #Bioinformatics #Genomics 𧬠π₯οΈ π§ͺ π π¨π¦
β¬οΈ
academic.oup.com/nar/article/...
19.09.2025 22:24 β π 2 π 0 π¬ 1 π 0
Not sure if this (these?) positions are filled yet, but as an ex-MSL tenured PI, and a fan of Micro, I can only highly recommend this position and department⦠Great city, great University, great campus, greatest students and great colleagues! Go for it!
12.09.2025 02:59 β π 0 π 0 π¬ 0 π 0
Microbiology and Immunology and the Michael Smith Labs are seeking candidates for an Assistant Professor of Teaching in STEM Public Engagement position.
Learn more and apply at: www.msl.ubc.ca/careers/
#IndigenousinSTEM #BlackInNature #WomenInSTEM #MinoritiesInSTEM #DiversityInSTEM #STEMEducation
22.07.2025 16:00 β π 17 π 24 π¬ 2 π 2
Ezra Klein thinks that βblack people are stupidβ and βgay people should be stoned to deathβ is practicing politics the βright wayβ
Can we stop pretending he is some political sage?
11.09.2025 11:30 β π 557 π 31 π¬ 1 π 0
My review of computational methods for anthropological genetics with @kwittadna.bsky.social is out for the Yearbook issue of AJBA.
We talk about all sorts of cool methods that YOU could use too!
Also check out this great figure we commissioned from @janey1216.bsky.social
doi.org/10.1002/ajpa...
20.03.2025 21:08 β π 14 π 12 π¬ 0 π 1
Stephen Jay Gould was born OTD in 1941.
βOrganisms are not billiard balls, propelled by simple and measurable external forces to predictable new positions on life's pool table.... Organisms have a history that constrains their future in myriad, subtle ways.β
π¦«π¦ππ±π§ ποΈπ§ͺ#HistSTM #PhilSci #EvoBio
10.09.2025 16:41 β π 158 π 44 π¬ 8 π 8
This is what this other PLOS CB paper is about! What @stefaniebutland.bsky.social said!
bsky.app/profile/bffo...
11.09.2025 12:15 β π 0 π 0 π¬ 0 π 0
LinkML is an open and extensible modeling framework for creating and validating computable, reusable, and interoperable data.
Documentation: https://linkml.io/linkml
Source code: https://github.com/linkml
Iβm over on Mastodon at https://scholar.social/@gedankenstuecke where I post from mostly
You can follow my bridged Mastodon account at @gedankenstuecke.scholar.social.ap.brid.gy
Researcher & #Luddite interested in theory & practice of #peerproduction. Loves everything open π: #openscience #citizenscience #opensource & [β¦]
[bridged from https://scholar.social/@gedankenstuecke on the fediverse by https://fed.brid.gy/ ]
Official account of the Bio-Ontologies and Knowledge Representation (BOKR) COSI, a community of the International Society for Computational Biology (ISCB).
The leading provider of open source workflow orchestration software for data pipelines, cloud infrastructure & collaboration. From the creators of @nextflow.io
The Bioinformatics and Functional Genomics Laboratory, led by Dr. Elsa GΓ³ngora Castillo, is part of the Department of Marine Resources at Cinvestav MΓ©rida in YucatΓ‘n, MΓ©xico.
πΌDOROTHY EU COFUND fellow
π΅Physoc Trustee
ππΌPronounced βFair-onβ
πKarolinksa Institute, Sweden
previously Maynooth Uni IRL, Uni of Galway IRL, QMUL London UK, Uni of Nottingham UK, TCD Dublin IRL
π₯Όobesity-assoc cancer immunology
β€οΈwild swimming
β§οΈShe/her
Tommy M. McGuire (Not that one. Nor that one.)
Coding bum, tetrapod. (he/him)
Bitterly cynical misanthrope. It's always more complicated. I apologize in advance; I tend to get too comfortable.
Called 'weird' by Kevin Kruse.
Camino a ser doctor en BiologΓa (CNB-CSIC), proyecto de poeta en los ratos libres. MelΓ³mano y peor cinΓ©filo de la historia, con la lista de pelis pendientes creciendo exponencialmente.
Supporting research to transform life, health and wellbeing. Weβre taking on three urgent health challenges: mental health, climate change & infectious disease.
We are the DS-I Africa Consortium funded by the National Institutes of Health. Please read the press release.
Part of Wellcome Sanger Institute and funded by Wellcome, we develop and deliver genomics-focused learning and training. Our events support scientific careers, as well as the equitable application of genomics into research and healthcare across the globe.
Computational cancer biology. #bioinformatics, #CancerGenomics. Interested in subtypes of #ColorectalCancer and chromosomal instability @oncology.ox.ac.uk 𧬠Previously @uoe-igc.bsky.social @roslininstitute.bsky.social @ESA.int @CERN.bsky.social π΄σ §σ ’σ ³σ £σ ΄σ ΏπͺπΊ he/him
Disease ecologist, Cary Institute of Ecosystem Studies. Zoonotic disease, predictive analytics, machine learning, AI. www.hanlab.science.
Professor of Ecology at the University of Georgia. Views are my own.
http://daphnia.ecology.uga.edu/drakelab/
PhD candidate in statistics at UBC.
Working on statistical genomics.
@biancarsbio's lucky husband.
giulianonetto.netlify.app
