FGED Society

Accelerating and supporting the effective sharing and reproducibility of functional genomics data. Tweets by @trutane, @bffo

[FGED Society @FGED]

Omics Data Sharing Resources, revised & updated, on the FGED Society's "afterlife" website: https://t.co/HbLr9zt1JA

Long Live Functional Genomics!🧬
#Reproducibility #OpenScience #OpenData #FunctionalGenomics #Omics #DataScience #DataSharing #Interoperable #Standards #FAIRdata

[Steve Chervitz Trutane ☮️ @trutane]

Huge loss for the biomedical data science community 😢 Atul Butte @atulbutte left us yesterday at the way-too-young age of 55.

Co-founder of @PersonalisInc (where I worked) + other biotechs, director of @UCSF_BCHSI, and a major #OpenScience advocate. He will be missed. #RIP🙏

[Awesomics @Awesomics]

Government word search is killing my cutting-edge research https://t.co/znGMdcBi3w — by @johnquackenbush

“…falling victim to a nationwide, indiscriminate destruction of university-based biomedical research…” due to the use of ‘forbidden’ words.

#NIHFundingCuts #DefendScience

[Stephen Turner 🦋 @stephenturner.us @strnr]

Benchmarking of variant calling software for whole-exome sequencing using gold standard datasets https://t.co/8j5gIPJIaD 🧬🖥️🧪

[Razia Aliani @RaziaAliani]

Are AI Tools Replacing Scientific Writing?
Here's what some leading scientists have to say ⤵
Repost & Save (with 𝘤𝘭𝘪𝘱𝘱𝘦.𝘮𝘦)

— Tools like ChatGPT are good helpers
(but poor creators)

— AI can speed up writing
(but it's not ready to take over scientific thinking).

— The real question isn't if we should use AI...
... but how to use it wisely!

𝐊𝐞𝐲 𝐁𝐞𝐧𝐞𝐟𝐢𝐭𝐬 𝐨𝐟 𝐀𝐈 𝐢𝐧 𝐒𝐜𝐢𝐞𝐧𝐭𝐢𝐟𝐢𝐜 𝐖𝐫𝐢𝐭𝐢𝐧𝐠 ⤵

𝗪𝗿𝗶𝘁𝗶𝗻𝗴 𝗔𝘀𝘀𝗶𝘀𝘁𝗮𝗻𝗰𝗲
— Helps break through writer's block
— Makes helpful suggestions for titles & abstracts
— Supports non-native English speakers with clear writing

𝗦𝘁𝗿𝘂𝗰𝘁𝘂𝗿𝗲 & 𝗥𝗲𝗳𝗲𝗿𝗲𝗻𝗰𝗲𝘀
— Breaks complex topics into manageable pieces
— Spots relevant papers you might have missed
— Helps organize thoughts & arguments

𝐌𝐚𝐣𝐨𝐫 𝐂𝐨𝐧𝐜𝐞𝐫𝐧𝐬

— AI can't do deep analysis or generate true insights
— Risk of shallow, cookie-cutter science writing
— Tools might generate false references or incorrect info
— Over-reliance could hurt students' learning

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[FGED Society @FGED]

Researchers
🧪 72% say there's a reproducibility crisis in biomedicine, 27% say it's significant
🧪 62% say pressure to publish ➡️ irreproducibility

Institutions
🥼 16% had procedures to enhance reproducibility
🥼 67% value new research > replication studies

#biomedicalResearch

[Stephen Turner 🦋 @stephenturner.us @strnr]

Biomedical researchers’ perspectives on the reproducibility of research https://t.co/AThPuySSAS 🧬🖥️

[FGED Society @FGED]

"quality imbalance btwn groups of samples can significantly reduce relevance of differential genes, reducing reproducibility btwn studies. Appropriate expt'l design & analysis methods can substantially reduce the problem."
#RNAseq #geneExpression
#transcriptome #transcriptomics

[Stephen Turner 🦋 @stephenturner.us @strnr]

Overlooked poor-quality patient samples in sequencing data impair reproducibility of published clinically relevant datasets https://t.co/Z4MqOfkgn2

[Retraction Watch @RetractionWatch]

Among 143 replications of 56 experiments, less than half of biomedical research from Brazil was replicable, researchers found.
https://t.co/GIKWmjCjbX

[Mick W@tson ↙️ @BioMickWatson]

I told a joke about data sharing, it's available upon request

[Lappalainen Lab @tuuliel_lab]

Excited to share our review paper in Cell! With @SashaGusevPosts @s_ramach @yang_i_li we discuss the genetic and molecular architecture of human traits, future opportunities and challenges and ways forward.

https://t.co/zVb8ImF4Y2

[cOAlition S @cOAlitionS_OA]

At @cOAlitionS_OA we are envisioning a community-based scholarly communication system fit for #OpenScience in the 21st century, based on five principles.
🟠https://t.co/0uGgNVR1ii
Follow this thread 🧵for a quick overview!
#OpenAccess #ResponsiblePublishing [1/7]

[Vince Buffalo @vsbuffalo]

Ah, I've wanted this table on data sharing repositories for a while! Very nice.
https://t.co/eXLQx0IvUe

[Vince Buffalo @vsbuffalo]

I think the sad actual answer to "What is the biggest open challenge in biology?" is:
1. Getting people to share data.
2. Structuring, organizing, and annotating data with metadata so it's useful.
3. Building higher-level abstractions so people can efficiently work with big data.

[Stephen Turner 🦋 @stephenturner.us @strnr]

Automated Bioinformatics Analysis via AutoBA 🤨 https://t.co/ah5DTjhx3J Prompt it with experimental designs, it provides "plans" and code. https://t.co/CZLU8pEs4c

[Awesomics @Awesomics]

GISAID in crisis: can the controversial COVID genome database survive? https://t.co/1U8mAL7jK6 ($)

@theosanderson had his @GISAID data access cut off w/out explanation, then restored after his story went ‘viral’👇

#SARSCoV2 #sequence
#Pathogen #DataSharing

[Manolis Kellis @manoliskellis]

Immensely proud to share our four papers on #SingleCell dissection of #Alzheimers Disease coming out in @CellCellPress today, reporting 2.3M #scRNA profiles and 850k #scATAC profiles across 427 post-mortem human brain samples from AD and non-AD donors in a wonderful #interdisciplinary collaboration with @DrLiHueiTsai between @MIT @MIT_Picower @MIT_CSAIL @BroadInstitute @RushUniversity
Paper 1: scRNA + vulnerability + resilience https://t.co/I7cmizyj9C
Paper 2: scATAC + GWAS + Epigenome Erosion https://t.co/bdtlu9bWDr
Paper 3: Microglia States + reprogramming https://t.co/NzEJF1wY3t
Paper 4: DNA damage + gene fusions https://t.co/hIY1tMMhLo
MIT News: https://t.co/oLDuBBb45S
Issue: https://t.co/Mup3orjhcl
News & Views: https://t.co/xQk5mepDqz

[Vince Buffalo @vsbuffalo]

I'm pleased to share a beta version of SciDataFlow, a command-line tool to track changes to data in research projects, push and pull data to remote repositories like Zenodo and FigShare, concurrently download tons of data, and more! https://t.co/bSwdrr0zXy

[Rebecca Barter @rlbarter]

Are you an R user who is interested in learning Python 🐍 ? My new blog post introducing Python from an R user's perspective might be just the launching point you need to get started on your journey 🛫

https://t.co/LDHzG2VlZm

#rstats #python #DataScience

[PNASNews @PNASNews]

Opinion piece: A better kind of #ReviewArticle? “Flexible synthesis” can deliver tailored and timely evidence for #research and #policy: https://t.co/CKjkxMdZb2 #MetaAnalysis #EvidenceBasedPolicy

[Folmer Fredslund @[email protected] @folfDK]

Interesting bit here on the requirements for data storage through FAIR principles and the economic and ecological costs of long-term storage of large quantities of data.

#FAIR
#OpenScience
#datascience
#structbio
https://t.co/KqMwE1aNnb

[FGED Society @FGED]

@GigaScience @serghei_mangul Nice work & important for improving #reproducibility & #FAIRdata in public omics data.

Interesting to compare with transcriptome data compliance with the #MINSEQE minimum info standard: https://t.co/qX2HDj33VH
(note: analysis was based on data ca. 2013)
#ISMB2022 #OpenScience