#bosc2023 — Public Fediverse posts
Live and recent posts from across the Fediverse tagged #bosc2023, aggregated by home.social.
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Our #BOSC2023 report has been published on F1000Research!
https://f1000research.com/articles/12-1568/v1You can also find it in the BOSC Collection https://f1000research.com/collections/bosc/about-this-collection which hosts posters and slides that were presented at BOSC, as well as these annual reports.
Big thanks to F1000Research for providing a home for these BOSC resources!
BOSC = #Bioinformatics #OpenSource Conference
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Our #BOSC2023 report has been published on F1000Research!
https://f1000research.com/articles/12-1568/v1You can also find it in the BOSC Collection https://f1000research.com/collections/bosc/about-this-collection which hosts posters and slides that were presented at BOSC, as well as these annual reports.
Big thanks to F1000Research for providing a home for these BOSC resources!
BOSC = #Bioinformatics #OpenSource Conference
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CoFest 2023 report by Jérémy Just: https://www.open-bio.org/2023/09/29/bosc-collaborationfest-2023-report/ #BOSC2023 #CollaborationFest
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CoFest 2023 report by Jérémy Just: https://www.open-bio.org/2023/09/29/bosc-collaborationfest-2023-report/ #BOSC2023 #CollaborationFest
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The talk videos from #BOSC2023 are now freely available on our YouTube channel https://youtube.com/playlist?list=PLir-OOQiOhXZ9xSyP2-6Yd2_8Cl6Q-lLv and also linked from our schedule page https://open-bio.org/events/bosc-2023/bosc-2023-schedule/#talks (you may have to scroll right to see them). 🍐📽️
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The talk videos from #BOSC2023 are now freely available on our YouTube channel https://youtube.com/playlist?list=PLir-OOQiOhXZ9xSyP2-6Yd2_8Cl6Q-lLv and also linked from our schedule page https://open-bio.org/events/bosc-2023/bosc-2023-schedule/#talks (you may have to scroll right to see them). 🍐📽️
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Thanks to @GigaScience for this great write-up about ISMB/BOSC, and for your rockin' birthday party, and of course, for being a sponsor of #BOSC2023! 💚🍐 http://gigasciencejournal.com/blog/going-large-language-models-at-ismb2023/
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Thanks to @GigaScience for this great write-up about ISMB/BOSC, and for your rockin' birthday party, and of course, for being a sponsor of #BOSC2023! 💚🍐 http://gigasciencejournal.com/blog/going-large-language-models-at-ismb2023/
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We encourage #BOSC2023 presenters to share their slides and posters on
#F1000Research, where they can appear in both the BOSC and ISMB collections. Just go to https://f1000research.com/collections/bosc and click the orange “Submit” button near the top right. -
We encourage #BOSC2023 presenters to share their slides and posters on
#F1000Research, where they can appear in both the BOSC and ISMB collections. Just go to https://f1000research.com/collections/bosc and click the orange “Submit” button near the top right. -
As I’m heading back to London from #BOSC2023, I can only reflect on much this conference means to me. If @BOSC didn’t exist my professional (and personal!) life would look quite differently and I’d be a lot poorer for it.
It was a blast to meet so many old friends again and make new ones, amongst a community of folks being so dedicated to and passionate about open science/data/source and doing ethical research more broadly.
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As I’m heading back to London from #BOSC2023, I can only reflect on much this conference means to me. If @BOSC didn’t exist my professional (and personal!) life would look quite differently and I’d be a lot poorer for it.
It was a blast to meet so many old friends again and make new ones, amongst a community of folks being so dedicated to and passionate about open science/data/source and doing ethical research more broadly.
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8/8 #BOSC2023 #ISMBECCB2023 summary.
Thank you everyone attending in person or online. We hope to have the talk videos freely available on our YouTube channel (https://www.youtube.com/@OBFBOSC), and encourage our presenters to share their slides and/or posters in our collection on F1000 http://f1000research.com/collections/bosc/
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8/8 #BOSC2023 #ISMBECCB2023 summary.
Thank you everyone attending in person or online. We hope to have the talk videos freely available on our YouTube channel (https://www.youtube.com/@OBFBOSC), and encourage our presenters to share their slides and/or posters in our collection on F1000 http://f1000research.com/collections/bosc/
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7/n #BOSC2023 #ISMBECCB2023 summary
The final session of talks, “FAIR and open data”, paved the way for a closing panel on Open and Ethical Data Sharing (https://www.open-bio.org/events/bosc-2023/bosc-2023-panel/) that expanded upon some of the points made by the two keynote speakers, including the observation that there’s no published ethical code for bioinformaticists, and the idea that we individually, and our scientific societies, can be advocates for better parctices in ethical data sharing.
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7/n #BOSC2023 #ISMBECCB2023 summary
The final session of talks, “FAIR and open data”, paved the way for a closing panel on Open and Ethical Data Sharing (https://www.open-bio.org/events/bosc-2023/bosc-2023-panel/) that expanded upon some of the points made by the two keynote speakers, including the observation that there’s no published ethical code for bioinformaticists, and the idea that we individually, and our scientific societies, can be advocates for better parctices in ethical data sharing.
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6/n #BOSC2023 #ISMBECCB2023 summary
The following session, #OpenScience, represented the breadth of BOSC topics, including talks relating to open infrastructures and ecosystems, citizen science, training, outreach, and reproducibility. After lunch, a joint session brought together BOSC and the Bio-Ontologies COSI for talks relating to standards (including, of course, #ontologies) and frameworks for open science.
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6/n #BOSC2023 #ISMBECCB2023 summary
The following session, #OpenScience, represented the breadth of BOSC topics, including talks relating to open infrastructures and ecosystems, citizen science, training, outreach, and reproducibility. After lunch, a joint session brought together BOSC and the Bio-Ontologies COSI for talks relating to standards (including, of course, #ontologies) and frameworks for open science.
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5/n #BOSC2023 #ISMBECCB2023 summary
... [BOSC keynote speaker] Joe Yracheta, the founder of the Native BioData Consortium, discussed our ethical responsibilities as people who work on open source tools and open bioinformatics research to ensure that indigenous data is ethically sourced and used.
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5/n #BOSC2023 #ISMBECCB2023 summary
... [BOSC keynote speaker] Joe Yracheta, the founder of the Native BioData Consortium, discussed our ethical responsibilities as people who work on open source tools and open bioinformatics research to ensure that indigenous data is ethically sourced and used.
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4/n #BOSC2023 #ISMBECCB2023 summary
The second day of BOSC started with a thought-provoking keynote by Joseph Yracheta entitled “The Dissonance between Scientific Altruism & Capitalist Extraction: The Zero Trust and Federated Data Sovereignty Solution”, which examined thorny questions about the current open data environment and how it impacts American Indian / Native American communities.
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4/n #BOSC2023 #ISMBECCB2023 summary
The second day of BOSC started with a thought-provoking keynote by Joseph Yracheta entitled “The Dissonance between Scientific Altruism & Capitalist Extraction: The Zero Trust and Federated Data Sovereignty Solution”, which examined thorny questions about the current open data environment and how it impacts American Indian / Native American communities.
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... [BOSC Opening Keynote speaker] Sara El-Gebali (@yalahowy), made many points that resonated with the BOSC audience, such as the need to revamp research reward systems to take into account open science practices, not just one-dimensional publication metrics. After the keynote, Day 1 of BOSC had themed sessions: Translational bioinformatics; Workflows; Data analysis and visualization; and a new (for BOSC) session on AI/ML.
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... [BOSC Opening Keynote speaker] Sara El-Gebali (@yalahowy), made many points that resonated with the BOSC audience, such as the need to revamp research reward systems to take into account open science practices, not just one-dimensional publication metrics. After the keynote, Day 1 of BOSC had themed sessions: Translational bioinformatics; Workflows; Data analysis and visualization; and a new (for BOSC) session on AI/ML.
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2/n #BOSC2023 #ISMBECCB2023 Summary
Our first keynote was by Sara El-Gebali (@yalahowy), who spoke inspiringly about “A New Odyssey: Pioneering the Future of Scientific Progress Through Open Collaboration,” with case studies showing how open collaboration can strengthen inclusive scientific communities and vice-versa. For example, 95.5% of genomic research participants in GWAS are people of European heritage; this has led to the development of drugs that don’t work for most of the people ...
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2/n #BOSC2023 #ISMBECCB2023 Summary
Our first keynote was by Sara El-Gebali (@yalahowy), who spoke inspiringly about “A New Odyssey: Pioneering the Future of Scientific Progress Through Open Collaboration,” with case studies showing how open collaboration can strengthen inclusive scientific communities and vice-versa. For example, 95.5% of genomic research participants in GWAS are people of European heritage; this has led to the development of drugs that don’t work for most of the people ...
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1/8 - #BOSC2023 #ISMBECCB2023 Summary
The 24th annual Bioinformatics Open Source Conference, BOSC 2023 (open-bio.org/events/bosc-2023), kicked off with a welcome from chair Nomi Harris, an overview of BOSC’s parent organization, the Open Bioinformatics Foundation, and a report about the pre-BOSC CollaborationFest (#CoFest), a collaborative work event (including but not limited to hacking) hosted by the nearby ENS de Lyon.
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1/8 - #BOSC2023 #ISMBECCB2023 Summary
The 24th annual Bioinformatics Open Source Conference, BOSC 2023 (open-bio.org/events/bosc-2023), kicked off with a welcome from chair Nomi Harris, an overview of BOSC’s parent organization, the Open Bioinformatics Foundation, and a report about the pre-BOSC CollaborationFest (#CoFest), a collaborative work event (including but not limited to hacking) hosted by the nearby ENS de Lyon.
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Unfortunately, the technical issue (Juno doesn't play well with Linux) was not resolvable; we regret that Brett was not able to livestream his #BOSC2023 talk. But you can now see it at https://youtube.com/watch?v=DzfQWFvBBMM&ab_channel=CuriiCorporation
@biocrusoe @tetron -
Unfortunately, the technical issue (Juno doesn't play well with Linux) was not resolvable; we regret that Brett was not able to livestream his #BOSC2023 talk. But you can now see it at https://youtube.com/watch?v=DzfQWFvBBMM&ab_channel=CuriiCorporation
@biocrusoe @tetron -
Photo of the moderator and in-person panelists (Joseph Yracheta is participating virtually) #BOSC2023
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Photo of the moderator and in-person panelists (Joseph Yracheta is participating virtually) #BOSC2023
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Closing #bosc2023 is a panel on open and ethical data sharing.
Panelists:
Sara El-Gebali
Bastian Greshake Tzovaras
Monica Munoz-Torres
Joseph M Yracheta
Verena Ras -
Closing #bosc2023 is a panel on open and ethical data sharing.
Panelists:
Sara El-Gebali
Bastian Greshake Tzovaras
Monica Munoz-Torres
Joseph M Yracheta
Verena Ras -
Junda Huang: The Trusted World of Corona project aimed to assemble a set of verifiable coronavirus knowledge. It works with the FAIR Data Cube tools, ISA/ISA+, and Phenopackets.
Here's the demo: -
Junda Huang: The Trusted World of Corona project aimed to assemble a set of verifiable coronavirus knowledge. It works with the FAIR Data Cube tools, ISA/ISA+, and Phenopackets.
Here's the demo: -
Anja Adamov: Sequence data resources don't all work with the same tools. But q2-fondue will fetch NCBI SRA records then convert into a standardized format, ready for further analysis. It can scrape from a Zotero citation library too. Get it here: https://github.com/bokulich-lab/q2-fondue
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Anja Adamov: Sequence data resources don't all work with the same tools. But q2-fondue will fetch NCBI SRA records then convert into a standardized format, ready for further analysis. It can scrape from a Zotero citation library too. Get it here: https://github.com/bokulich-lab/q2-fondue
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Xiaofeng Liao: FAIR Data Cube is tools and services for standardizing multi-omics metadata, data transformation, and federated computing.
What does it have to do with cubes? (A cube has multiple sides, like multi-omics)
Take a look: https://github.com/Xomics/FAIRDataCube -
Xiaofeng Liao: FAIR Data Cube is tools and services for standardizing multi-omics metadata, data transformation, and federated computing.
What does it have to do with cubes? (A cube has multiple sides, like multi-omics)
Take a look: https://github.com/Xomics/FAIRDataCube -
Tarcisio Mendes de Farias: Bioinformatics knowledge bases are built for specific communities. Reusability of those resources can be improved though better interoperability, e.g., with Bgee, interfacing with Wikimedia and GeneCards promotes reuse. Same for compatibility with Schema.org, since that enables Google Dataset Search. Take home message: partial interoperability is better than none.
#ismbeccb2023 #bosc2023 -
Tarcisio Mendes de Farias: Bioinformatics knowledge bases are built for specific communities. Reusability of those resources can be improved though better interoperability, e.g., with Bgee, interfacing with Wikimedia and GeneCards promotes reuse. Same for compatibility with Schema.org, since that enables Google Dataset Search. Take home message: partial interoperability is better than none.
#ismbeccb2023 #bosc2023 -
Jackson Callaghan: Let's integrate the world's biomedical knowledge into a graph! (Yes, I agree!) BioThings is working on that, and if you want to query their graph, you can take advantage of its semantic annotations.
https://explorer.biothings.io/
#ismbeccb2023 #bosc2023 -
Jackson Callaghan: Let's integrate the world's biomedical knowledge into a graph! (Yes, I agree!) BioThings is working on that, and if you want to query their graph, you can take advantage of its semantic annotations.
https://explorer.biothings.io/
#ismbeccb2023 #bosc2023 -
Bhavesh Patel: How do we make research software reusable? Actionable advice is out there in the FAIR-BioRS guidelines, an effort started at BOSC CoFest 2022.
See http://github.com/fair-biors -
Bhavesh Patel: How do we make research software reusable? Actionable advice is out there in the FAIR-BioRS guidelines, an effort started at BOSC CoFest 2022.
See http://github.com/fair-biors -
Matthew Crown: Microbiome composition changes with geographic location, so you probably want to annotate that metadata consistently, right? OMEinfo helps to link and visualize location data.
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Matthew Crown: Microbiome composition changes with geographic location, so you probably want to annotate that metadata consistently, right? OMEinfo helps to link and visualize location data.
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Vasundra Touré: the Swiss Personalized Health Network involves numerous terms and relationships. Conveniently, it's all modeled with an RDF schema and linked to a semantics dataset.
https://sphn.ch/network/data-coordination-center/the-sphn-semantic-interoperability-framework/ -
Vasundra Touré: the Swiss Personalized Health Network involves numerous terms and relationships. Conveniently, it's all modeled with an RDF schema and linked to a semantics dataset.
https://sphn.ch/network/data-coordination-center/the-sphn-semantic-interoperability-framework/ -
Justin Reese: do you want to build a knowledge graph but don't know where to start? Would you like it to be compatible with other graphs, queryable, and ready for machine learning? You'll probably find KG-Hub useful.
Read more at http://kghub.org -
Justin Reese: do you want to build a knowledge graph but don't know where to start? Would you like it to be compatible with other graphs, queryable, and ready for machine learning? You'll probably find KG-Hub useful.
Read more at http://kghub.org -
Note that Brett Smith's talk, "Realizing FAIR Principles For Data and Workflows with the Arvados Platform", which was supposed to be yesterday, is rescheduled due to technical issues to today at 15:30 (end of joint #BOSC2023 #bioontologies session)
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Note that Brett Smith's talk, "Realizing FAIR Principles For Data and Workflows with the Arvados Platform", which was supposed to be yesterday, is rescheduled due to technical issues to today at 15:30 (end of joint #BOSC2023 #bioontologies session)
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Sierra Moxon: In the real world, data is messy! We can share vocabularies, but that's not enough. You can be an expert in one data framework but still can't communicate with those using other standards and models. It's a job for the universal converter that is LinkML.
See http://linkml.io
#ismbeccb2023 #bosc2023 -
Sierra Moxon: In the real world, data is messy! We can share vocabularies, but that's not enough. You can be an expert in one data framework but still can't communicate with those using other standards and models. It's a job for the universal converter that is LinkML.
See http://linkml.io
#ismbeccb2023 #bosc2023 -
Now in the joint #bosc2023 and #bioontologies session:
Herve Menager presents the Research Software Ecosystem. Centralized software metadata from federated sources. It's all on GH at https://github.com/research-software-ecosystem/content -
Now in the joint #bosc2023 and #bioontologies session:
Herve Menager presents the Research Software Ecosystem. Centralized software metadata from federated sources. It's all on GH at https://github.com/research-software-ecosystem/content -
Finishing up experiments in a boiling lab, living vicariously through wonderful people live tooting #BOSC2023 #ismbeccb2023 Thanks everyone!
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Lisanna Paladin: EMBL has high turnover by design, so there's a constant need for flexible, on-demand training.
That's what http://bio-it.embl.de does.
#ismbeccb2023 #bosc2023