#elixir

2023-01-12

Aedin Culhane (12:00:57): > @Aedin Culhane has joined the channel

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Aedin Culhane (12:02:22): > ELIXIR ALL Hands Meeting Dublin 5-8th June 2023Link to submit abstractInformation about meeting and abstract review criteria - Attachment (ELIXIR): ELIXIR All Hands 2023 > The ELIXIR All Hands 2023 will be held in the Dublin Convention Centre, Ireland. The 9th ELIXIR All Hands meeting will take place 5-8 June 2023 in Ireland. The meeting brings together members of the

Aedin Culhane (12:02:42): > * There are 4 themes to the meeting this year’’Science - Enabling scientists to access and analyse life science data” > * ’’Technology - Delivering services to support federated data management and analytics” > * “Nodes - Equipping national Nodes for successful long-term operations” > * “People - Developing people and capacity to benefit science and society”

Aedin Culhane (12:03:04): > We could submit under science or people

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Aedin Culhane (12:07:16): > Session/workshops are 90 mins long and the submission deadline isMonday 23 January, 2023. For submission, we need a title, abstract (400 words) and a list of presenters of which 2 need to attend in person. Leo, Maria and I can most likely attend in person, so we have sufficient to submit an abstract for a session. We just need to define the abstract and session

Aedin Culhane (12:13:27): > There are currently 239 training materials from Bioconductor on theELIXIR training platform - Attachment (tess.elixir-europe.org): TeSS (Training eSupport System)

Aedin Culhane (12:15:27): > with 0 upcoming events and 1 past event (which was a Bioc2020 conference workshop?)

Aedin Culhane (12:20:16): > Slidespresented at last year’s meeting about the ELIXIR training portaland its abstract/title/presenters

Aedin Culhane (12:29:40): > I think we should think about leverages some of the ELIXIR resources for our global training platform … > > I like their dashboard…https://training-metrics-dev.elixir-europe.org/dashboardCourses are registered via a simple web app (I recently did an ELIXIR training courses.. its was just a standard training course but it was registered with ELIXIR.. the form took 2 min to fill in). The course info is represented via their bioschema (https://bioschemas.org) and is available to the API which present course info/dashboard etc. > > They also have course metrics and surveys… - Attachment (bioschemas.org): Bioschemas - Bioschemas > Bioschemas relies and extends from schema.org and aims to reuse existing standards and reach consensus among a wide number of life sciences organizations and communities.

Aedin Culhane (12:29:54): > https://training-metrics-dev.elixir-europe.org/dashboard

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Leo Lahti (14:41:01) (in thread): > I like both.

Leo Lahti (14:42:18): > Great. I have not been in events making general Bioc outreach. Would be nice to know if this is more familiar to some of you, and if there is some earlier material/experiences that can be utilized.

Leo Lahti (14:42:48): > Or if you have a vision.

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Maria Doyle (17:38:18): > Not a concrete vision for the workshop just some thoughts, > > Elixir are finalising their scientific programme for 2024-2028 this yearhttps://elixir-europe.org/about-us/what-we-do/2024-28-programmeThey have an interest in collaborations with international organisations of value to their members (Bioc is not listed on that page, could ite be)https://elixir-europe.org/events/consultation-event-international-engagementThere is an ELIXIR Galaxy communityhttps://elixir-europe.org/communities/https://galaxyproject.org/news/2022-06-21-elixirah22/But no ELIXIR Bioconductor community, should there be? > > Wondering if the workshop should have 2 parts 1- highlight what Bioconductor is doing that overlaps with Elixir interests and 2- have time (30 min) for discussion/breakout session like the workshop Aedin linked to herehttps://docs.google.com/document/d/1vlHODVnN9RFTp2fr2NCcLV4ujb8Js3EH6NqXHfP_F9E/edit#? e.g. “Engagement between Bioconductor and ELIXIR”? to get input on how Bioc could most usefully mutually engage with ELIXIR. Also may help get Bioconductor on the radar for their scientific programme for 2024-2028 which could help with growing and strengthening Bioc community. > > Potential overlapping areas of interest we could perhaps discuss in workshop from viewingElixir 2021 report(might be wrong and/or more I missed) > Platformshttps://elixir-europe.org/platformsTools - benchmarking tools & workflows, EDAM, biotools > Training - workshops, materials, events, TESS, > Communities -https://elixir-europe.org/communitiesSingle Cell Omics, Proteomics - Attachment (ELIXIR): ELIXIR Programme for 2024-2028 | Consultation event on international engagement > Objectives This 2 hour online event aims to provide ELIXIR Nodes with an opportunity to influence international engagement as part of the upcoming ELIXIR Programme for 2024-2028. The event’s outputs - Attachment (galaxyproject.org): Galaxy taking part @ Elixir All Hands 2022 > During 6-9th of June, members of the European Galaxy team travelled to Amsterdam to join the ELIXIR All Hands meeting 2022 where we joined other colleagues from ELIXIR-DE.

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2023-01-13

Leo Lahti (02:19:24): > Sounds good to me at least.

Charlotte Soneson (02:35:56) (in thread): > Regarding a potential Bioconductor ELIXIR Community - if we decide to give this a try, I think it would make sense to talk to the Galaxy team again to get their experience (we have touched upon it on a couple of occasions already). It takes a decent amount of time to get a new community set up (for the recent single-cell community I’d say it took about 2.5 years from the first concrete document was initialised to the approval - I’m not sure if this is representative, but in any case the application has to go through a bunch of different stages).

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Vince Carey (19:18:35): > @Wolfgang Huber^^

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2023-01-17

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2023-01-18

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2023-01-20

Aedin Culhane (17:41:45): > I updated thegoogle doc.. welcome your suggestions and contributions. The submission deadline isMonday 23 January, 2023. For submission, we need a title, abstract (400 words) and a list of presenters of which 2 need to attend in person. Please add your name if you are a member of ELIXIR and wish to contribute.

2023-01-21

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2023-01-22

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Maria Doyle (16:02:12): > Following on from Aedin’s message above, we plan to submit the abstract in thegoogle doc~12pm GMT tomorrow Monday 23rd Jan, if anyone wants to add more comments please do before then:pray:

2023-01-23

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Aedin Culhane (07:39:17): > <!channel>We are submitting the abstract in thegoogle docshortly. Please review and add final comment

Maria Doyle (09:34:40): > Ok submitted, says will be notified on outcome Feb 10th. Thanks all!

2023-01-27

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2023-01-31

Aedin Culhane (07:01:37): > EU folks… has anyone experience in microcredential courses?

2023-02-06

Maria Doyle (10:37:40): > Good news, workshop has been accepted:tada: > > I am pleased to inform you that your workshop submission (Opportunities for Bioconductor and ELIXIR communities to co-develop training infrastructures) has been accepted for the ELIXIR All Hands Meeting 2023. > > > > Guidelines for further preparation are attached and will shortly be posted on the conference website. As a workshop lead you and your named co-lead have been pre-registered for the event. Other speakers will need to register through the normal links, registration will open at the end of February. > > > > We look forward to seeing you in Dublin Convention Centre in June.

2023-02-10

Daniel Adediran (19:44:13): > @Daniel Adediran has joined the channel

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2023-02-11

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2023-02-12

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2023-02-17

Frederick Tan (10:22:00): > Perhaps relevant? Hybrid ELIXIR Single-Cell Omics Community workshop in Geneva on March 21/22 for data analysis trainershttps://bit.ly/SCOtrainerWorkshop2023

2023-02-20

Aedin Culhane (12:19:52): > @Charlotte SonesonWhat is the overlap between GOBLET and ELIXIR?

2023-02-21

Charlotte Soneson (02:48:33) (in thread): > Not sure I have the full picture/answer here, but they’re collaborating on training, see e.g.https://elixir-europe.org/system/files/goblet-elixir_partnership-final.pdf

2023-02-27

Aedin Culhane (05:42:03): > FYI. See calls for proposals for Elixir biohackathon (30 Oct-3 Nov),Hacking projects (biohackathon-europe.org)A hackathon is not necessarily coding, I think it can sometimes be e.g. developing protocols and standards, etc relevant to coding > > > SCOPE > BioHackathon activities are driven by practical sessions where people gather, discuss, and implement ideas and projects during intensive and productive coding sessions. The topics will be aligned to challenges proposed byELIXIR Platforms,ELIXIR Communities, and/orFocus Groups, and a set of common challenges proposed by the sisterBioHackathonorganised in Japan. > GOALS > · Advance the development of an open source infrastructure for data integration to accelerate scientific innovation. We will focus on technology implementations such as FAIR, identifiers, metadata standards, ontologies and metadata catalogues that support the operations acrossELIXIR Platforms,CommunitiesandFocus Groups. > · Engage technical people in the bioinformatics community inside and outside ELIXIR to work together on topics of common interest aligned to ELIXIR activities > · Strengthen the interactions with ELIXIR Platforms, Communities and Focus Groups to establish and reinforce collaborations through hands-on programming activities. - Attachment (biohackathon-europe.org): Hacking projects > Barcelona 30 October - 3 November 2023 - Attachment (biohackathon.org): > BioHackathon

2023-03-03

Maria Doyle (09:05:02): > <!channel>our Elixir All Hands workshop “Opportunities for Bioconductor and ELIXIR communities to co-develop training infrastructure” will beTuesday June 6th 11-12.30pm GMT.If you’re interested to take part inthe agendaplease let me know as we’ll start populating it in the next week or so.

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2023-04-03

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2023-04-05

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2023-04-06

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2023-04-12

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2023-05-03

Maria Doyle (13:21:35): > <!channel>if you would like to contribute (either in-person in Dublin or remotely) to the Elixir All Hands workshop “Opportunities for Bioconductor and ELIXIR communities to co-develop training infrastructure” on June 6th 11-12.30pm GMT please let me know.

2023-05-11

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2023-06-01

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2023-06-06

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2023-06-07

Aedin Culhane (09:11:56): > ELIXIR single cell ’omics community have a co-lead position open if any is interested

Aedin Culhane (09:13:25): > If anyone wants to assist Maria in plans to update connectivity between Tess and Bioconductor by building support for Bioschema, let Maria knowhttps://tess.elixir-europe.org/content_providers/bioconductor - Attachment (tess.elixir-europe.org): Bioconductor > Open development software project, based on the R programming language, > providing tools for the analysis of high-throughput genomic data. The project aims to enable > interdisciplinary research, collaboration and rapid development of scientific software.

Aedin Culhane (09:13:45): > https://tess.elixir-europe.org/materials/getting-started-with-bioschemas

U023JDZ6Q4S (09:20:06): > there is some discussion in<#C0262CVJSC9>on this topic too:slightly_smiling_face:https://elixir-europe.slack.com/archives/C0262CVJSC9/p1686061370798999 - Attachment: Attachment > We should get in contact with Maria Doyle to discuss about Bioschemas scraping of Bioconductor training material. It looks like a very nice opportunity to work together!

2023-06-08

U02433X2S76 (07:30:12): > <@U04T1MQNFN1>looks like you have a busy future ahead of you. Obviously we need a bit of time to develop these initial ideas and plans but it would be really good if at some point just after summer we could dedicate some time to Bioconductor and Elixir collaborating in one of the regular Training Platform meetings.

U04T1MQNFN1 (09:37:46): > That would be great

2023-06-09

Aedin Culhane (17:16:43): > Biohackathon projects for Barcelona.https://biohackathon-europe.org/projects.html - Attachment (biohackathon-europe.org): Hacking projects > Barcelona 30 October - 3 November 2023

2023-06-13

Maria Doyle (13:15:44): > Bioconductor website survey is now LIVE and posted about in Bioconductor Slack and Elixir Slack#generalchannels. > * https://community-bioc.slack.com/archives/C35G93GJH/p1686661875820929 > * https://elixir-europe.slack.com/archives/C01DPT2E2DU/p1686674062828269 > Posting survey link here as<@U02433X2S76>, thanks for your previous feedback, this is the official survey link if you want to share with your usershttps://t.maze.co/169169456

U02433X2S76 (13:38:23): > Thanks. I’ll share it about.

2023-08-10

U059439UP70 (08:57:34): > Microbiome data science with R/Bioconductor course in****:****University of Bergen October 9-12, 2023:https://norbis.w.uib.no/microbiome-data-science-with-r-bioconductor/

2023-09-11

U059AN3RK98 (12:09:21): > Nice slides set on ELIXIR TESS historyhttps://docs.google.com/presentation/d/1Qt9eD_NRPItBa0WpkyA2ejdPKrsPZlnb/edit#slide=id.p5

U059AN3RK98 (12:10:45): > <!channel>Hope to see you EuroBioc next week in Brussels … Should be have a BOFI..

U059AN3RK98 (12:11:20): > deadline for submission is Sept 20https://eurobioc2023.bioconductor.org/submissions/ - Attachment (eurobioc2023.bioconductor.org): Submissions > Submissions

Leo Lahti (12:43:09): > I can only be in Gent on Wed-Thu, so Fri BoF I will miss.

2023-09-12

Aedin Culhane (04:28:33): > The ELIXIR-Germany BioHackathon projects were just announced and we are back again this year with SpaceHack 2.0! This time we focus on establishing systematic benchmarking for spatial cluster/domain identification in spatial transcriptomics data. Please spread the word to your groups and networks – those interested can register via this link:https://www.denbi.de/helpdesk?option=com_rsform&view=rsform&formId=7. - Attachment (denbi.de): HelpDesk > The ‘German Network for Bioinformatics Infrastructure – de.NBI’ is a national, academic and non-profit infrastructure supported by the Federal Ministry of Education and Research providing bioinformatics services to users in life sciences research and biomedicine in Germany and Europe. The partners organize training events, courses and summer schools on tools, standards and compute services provided by de.NBI to assist researchers to more effectively exploit their data.

2023-10-09

U059AN3RK98 (09:52:46): > @Dario Righellihas questions about the Space Biohackathonhttps://cloud.denbi.de/about/testimonials/denbi-biohackathon-spacehack-project/. Connecting you<@U027T75LNSC>

Dario Righelli (10:12:08) (in thread): > Thanks@Aedin Culhane, I was interested to have a few more details on how the hackathon is organised and/or if there are already some defined aims for it. > Thanks!

U059AN3RK98 (12:39:43): > For Bioconductor folks..https://elixir-europe.org/events/elixir-single-cell-omics-community-f2fhybrid-meeting-0 - Attachment (ELIXIR): ELIXIR Single Cell Omics Community F2F/hybrid meeting > This year, we are combining the annual community gathering with the FAIR Data Management Workshop. The annual meeting is scheduled for October 18th and will be hosted at the EMBL-EBI Campus in

2023-10-12

U027T75LNSC (07:01:43) (in thread): > Oops - I missed this. > Thanks for reaching out! The hackathon itself is organised by de.NBI (the German Network for Bioinformatics, a.k.a ELIXIR-Germany) as part of theGerman BioHackathon. They deal with all the organisation aspects (food, location, registration, …). I deal with organizing and running the project covering the topics, providing centralized cloud compute, and day-to-day entertainment/motivation. > We have another iteration to take place this year in December:https://spatialhackathon.github.io/If you are interested in the administrative/technical organisation of the hackathon then you want to contact de.NBI (contact@denbi.de), otherwise we can chat further about the SpaceHack v1/v2 projects:slightly_smiling_face:

2023-12-30

Aedin Culhane (09:32:25): - Attachment (datascience.cancer.gov): Sharing Cancer Research Software? NIH Wants to Hear from You! | CBIIT > Are you working with source codes, algorithms, workflows, and other software in your cancer research? NIH wants to hear from you! Respond today to help NIH develop new best-practice guidelines.

2024-02-04

Leo Lahti (09:15:42): > European Conference on Computational Biology (ECCB) 2024 will take place in Turku, Finland on Sep 16-20: > CfP:https://eccb2024.fi/callsThere is a special “ELIXIR Communities Track”. As this is my home town & I am in the local org. committee, I will be present in any case. Hence I was thinking whether The ELIXIR Bioconductor Community should consider something here. Is anyone else planning to join? The DL for workshops and tutorials is Feb 15, proceedings March 14, highlight talks and posters Apr 23.

2024-02-09

Levi Waldron (09:23:28): > @Levi Waldron has left the channel

2024-03-26

U031FT693FD (13:26:18): > Hi everyone, is there anyone who have experience with developing R bioconductor package?

Vince Carey (13:36:46): > <@U031FT693FD>Consider visiting#developers-mentorshipand#developers-forum

U031FT693FD (13:47:11): > I do not have access@Vince Carey, both are private - File (PNG): image.png

Maria Doyle (13:51:52): > <@U031FT693FD>actually#developers-mentorshipand#developers-forumare public channels within the Bioconductor Slack workspace. This channel where you’ve posted your question is a shared channel between Bioconductor and Elixir workspaces. To access the channels Vince mentioned, you’ll need to join the Bioconductor Slack through this link:https://slack.bioconductor.org/. Once you’re in, you should hopefully get the help and guidance you’re looking for regarding R Bioconductor package development. Hope to see you there!

U031FT693FD (13:56:44): > Ah, I thought it is in ELIXIR … Thanks for pointing this out :)

2024-05-18

Aedin Culhane (11:02:45) (in thread): > I was thinking of going but not confirmed

2024-06-02

Aedin Culhane (14:44:47): > :mega:EuroBioC2024 Registration is Open!:tada:We are excited to share that registration for EuroBioC2024 is open! Join us for the European Bioconductor conference in beautiful Oxford, UK, from September 4-6. Secure your spot and take advantage of discounted accommodation by registering now!:point_right:https://eurobioc2024.bioconductor.org/registration/Help spread the word!:pray: > * https://www.linkedin.com/feed/update/urn:li:activity:7202223655781580800 > * https://genomic.social/@bioconductor/112534743328078110 - Attachment (eurobioc2024.bioconductor.org): Registration > Registration - Attachment (linkedin.com): Bioconductor on LinkedIn: #eurobioc2024 #bioinformatics #rstats #bioconductorcommunity > :mega: Registration for EuroBioC2024 is open! :tada: > > Join us for the European Bioconductor conference in beautiful Oxford, UK, from September 4-6. This event focuses… - Attachment (genomic.social): Bioconductor (@bioconductor@genomic.social) > Attached: 1 image > > :mega: Registration for EuroBioC2024 is open! :tada: > > Join us for the European Bioconductor conference in beautiful Oxford, UK, from September 4-6. This event focuses on cutting-edge bioinformatics and data analysis using R and Bioconductor. :computer::dna: Secure your spot and take advantage of discounted accommodation by registering now! > > :point_right: Register here: https://buff.ly/4aHLu7m > > #EuroBioC2024 #Bioinformatics #RStats #BioconductorCommunity

2024-06-27

U059AN3RK98 (07:07:22): > For anyone at Galaxy,<@U04T1MQNFN1>will be speaking today. - File (PNG): image.png - File (PNG): image.png

U059AN3RK98 (07:15:39): - Attachment: Attachment > @U05EV1P8L2X has joined the channel

2024-09-15

Aedin Culhane (14:02:08): > https://elixir-europe.org/sites/default/files/documents/Final-Memorandum-of-Agreement-between-ELIXIR-NIH_ODSS.pdf

2024-09-20

Aedin Culhane (09:16:26): > Hi, Should we write a blog post forhttps://blog.bioconductor.org/announcing the MoU and listing the ELIXIR/NIH projects in which Bioconductor is involved. - Attachment (blog.bioconductor.org): Bioconductor community blog > A blog for the Bioconductor community!

2024-12-10

U073FHNT4MB (04:51:00): > Hi there! Just randomly discovered the existence of this channel:sweat_smile:

Maria Doyle (12:32:07): > :wave:hi Claire, glad you found it:relaxed: