September 2020 - Neurofedora - Fedora mailing-lists

[Fwd] COMBINE 2020: Registration open; Call for abstracts, breakouts and tutorials
by Ankur Sinha 29 Sep '20

29 Sep '20

Hello, Late registration for the COMBINE meeting is still open. Registration is free, so it's really worth registering and checking out the agenda. There are sessions related to some NeuroFedora packages, COPASI for example. ----- Forwarded message ----- > Date: Wed, 5 Aug 2020 12:45:09 +0100 > Subject: [Neuroml-technology] COMBINE 2020: Registration open; Call for abstracts, breakouts and tutorials > > Dear NeuroML community, > > The "Computational Modeling in Biology" Network (COMBINE) is an initiative > to coordinate the development of the various community standards and formats > in systems biology and related fields. COMBINE 2020 will be a workshop-style > online event with oral presentations and breakout sessions. The five meeting > days will include talks about the COMBINE standards and associated or > related standardization efforts, presentations of tools using these > standards, breakout sessions for detailed discussions as well as tutorials. > > Due to the current COVID-19 situation, the on-site meeting in Connecticut > (USA) had to be cancelled. Therefore, COMBINE 2020 will be an online > (virtual) meeting from October 5th (Monday) to October 9th (Friday). It will > provide a schedule which takes into account all time zones around the world, > a real 24 hour conference. The meeting will be free of charge. > > IMPORTANT DATES > --------------- > > Registration deadline: 1st Sept 2020 > Abstract/breakout/tutorial submission deadline: 1st Sept 2020 > Notification of acceptance of abstracts/breakout/tutorial: 14th Sep 2020 > COMBINE Workshop: 5th-9th Oct 2020 > > REGISTRATION > ------------------ > > Registration for the meeting is open and is free. Please register at the > link below as soon as possible. This will help us plan the schedule and > match your interests to the timing of the breakouts, etc. > > Registration: https://forms.gle/3Netp5WBCupeeu1H6 > > CALL FOR ABSTRACTS > ------------------ > > We solicit high-quality abstracts, to be refereed by the COMBINE > Coordinators, for online presentation at the Workshop. Abstracts will appear > on the COMBINE website only, there will be no formal publication. > > Abstract submissions: https://forms.gle/gKVEWxV6mkYuwa8VA > > CALL FOR BREAKOUT SESSIONS > ------------------ > > All attendees can suggest breakout sessions for detailed discussions of > certain aspects of one or several of the COMBINE standard(s), discussions on > metadata and semantic annotations (format-specific or overarching), > discussions on the application and implementations of the COMBINE standards, > or any other topic relevant for the COMBINE community. The topics for those > breakout sessions, and the time slots which would suit their communities can > be submitted at the link below. > > Breakout suggestions: https://forms.gle/YCN6PtN5Ws3sSFPWA > > CALL FOR TUTORIALS > ------------------ > > If there are tutorials on tools, standards or resources (or any other topic) > which would be relevant for the COMBINE community (see Topics of Interest > below), these can be proposed at the link below (same link as for breakout > sessions). > > Tutorial suggestions: https://forms.gle/YCN6PtN5Ws3sSFPWA > > TOPICS OF INTEREST > ------------------ > > Topics of interest for the meeting include, but are not limited to: > > - Data exchange, pipelines and model standards for systems and synthetic > biology > - Visualization and graphical notation standards for systems and synthetic > biology > - Standards for sharing and analysing biological pathway data > - Standards for computational biological models and modelling support > - Metadata description and model annotation in COMBINE standard formats > - Implementation of COMBINE standards in tools, databases and other > resources > - Integrated model and data management for systems and synthetic biology > - Standardization of Artificial Intelligence approaches in biological > modelling > - Emerging standardization needs and multicellular modeling > - Community aspects of COMBINE > > More on the COMBINE standards at http://co.mbine.org/standards > > Best regards, > The COMBINE Coordinators > > Gary Bader, University of Toronto, Canada > Padraig Gleeson, University College London, UK > Martin Golebiewski, Heidelberg Institute for Theoretical Studies (HITS), > Germany > Thomas Gorochowski, University of Bristol, UK > Sarah Keating, University College London, UK > Matthias König, Humboldt University Berlin, Germany > Chris J. Myers, University of Colorado Boulder, USA > David Nickerson, University of Auckland, New Zealand > Falk Schreiber, University of Konstanz, Germany > Dagmar Waltemath, University of Greifswald, Germany > http://co.mbine.org/about > > ----- End forwarded message ----- -- Thanks, Regards, Ankur Sinha "FranciscoD" (He / Him / His) | https://fedoraproject.org/wiki/User:Ankursinha Time zone: Europe/London

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I want to be a part of NeuroFedora!
by Vivek Sharma 24 Sep '20

24 Sep '20

Hi, I'm Vivek (They/Their). I'm currently working as a research assistant at the National Brain Research Centre, India. My work revolves around signal processing, machine learning, and mathematical modeling. I'm also a Linux and python enthusiast and have been using fedora for five years now. I came across NeuroFedora, and I found it super exciting as it integrates both the things I have been involved with for so long. So, here I'm looking forward to contributing and have a fantastic time with y'all. Thanks -- Vivek Sharma

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Next Open NeuroFedora Meeting: 1300 UTC on Monday, 21st September
by Ankur Sinha 21 Sep '20

21 Sep '20

Hello everyone, Please join us at the next Open NeuroFedora team meeting next week on Monday 21 September at 1300UTC in #fedora-neuro on IRC (Freenode). The meeting is a public meeting, and open for everyone to attend. https://webchat.freenode.net/?channels=#fedora-neuro The channel is bridged to Telegram, so you can also join us there on the @NeuroFedora group: https://t.me/NeuroFedora You can convert the meeting time to your local time using this command in a terminal: $ date --date='TZ="UTC" 1300 next Mon' or you can use this link: https://www.timeanddate.com/worldclock/fixedtime.html?msg=NeuroFedora+Meeti… The meeting will be chaired by @ankursinha. The agenda for the meeting is: - New introductions and roll call. - Tasks from last week's meeting: https://meetbot.fedoraproject.org/teams/neurofedora/neurofedora.2020-09-07-… - Open Pagure tickets: https://pagure.io/neuro-sig/NeuroFedora/issues?status=Open&tags=S%3A+Next+m… - Open bugs check: https://tinyurl.com/neurofedora-bugs - CompNeuro lab compose status check for F33/F34. - Neuroscience query of the week. - Next meeting day, and chair. - Open floor. We hope to see you there! You can learn more about NeuroFedora here: https://neuro.fedoraproject.org -- Thanks, Regards, Ankur Sinha "FranciscoD" (He / Him / His) | https://fedoraproject.org/wiki/User:Ankursinha Time zone: Europe/London

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Re: Orphaned packages looking for new maintainers
by Ankur Sinha 15 Sep '20

15 Sep '20

Hi folks, Just an update on the latest orphaned packages report: On Tue, Sep 15, 2020 00:08:13 +0200, Miro Hrončok wrote: > The following packages are orphaned and will be retired when they > are orphaned for six weeks, unless someone adopts them. If you know for sure > that the package should be retired, please do so now with a proper reason: > https://fedoraproject.org/wiki/How_to_remove_a_package_at_end_of_life > > Note: If you received this mail directly you (co)maintain one of the affected > packages or a package that depends on one. Please adopt the affected package or > retire your depending package to avoid broken dependencies, otherwise your > package will be retired when the affected package gets retired. > > Request package ownership via the *Take* button in he left column on > https://src.fedoraproject.org/rpms/<pkgname> > > Full report available at: > https://churchyard.fedorapeople.org/orphans-2020-09-14.txt > grep it for your FAS username and follow the dependency chain. > > For human readable dependency chains, see https://packager.fedorainfracloud.org/ > For all orphaned packages, see https://packager.fedorainfracloud.org/orphan > ><snip> > > neuro-sig: sonatype-oss-parent > ><snip> sonatype-oss-parent is required by neurord, which is FTBFS because of a missing Java dependency already. I expect neurord will be orphaned/retired soon and like other Java packages, we may end up temporarily providing it via the COPR. -- Thanks, Regards, Ankur Sinha "FranciscoD" (He / Him / His) | https://fedoraproject.org/wiki/User:Ankursinha Time zone: Europe/London

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Next Open NeuroFedora Meeting: 1300 UTC on Monday, 7th September
by Ankur Sinha 07 Sep '20

07 Sep '20

Hello everyone, Please join us at the next Open NeuroFedora team meeting next week on Monday at 1300UTC in #fedora-neuro on IRC (Freenode). The meeting is a public meeting, and open for everyone to attend. https://webchat.freenode.net/?channels=#fedora-neuro The channel is bridged to Telegram, so you can also join us there on the @NeuroFedora group: https://t.me/NeuroFedora You can convert the meeting time to your local time using this command in a terminal: $ date --date='TZ="UTC" 1300 next Mon' or you can use this link: https://www.timeanddate.com/worldclock/fixedtime.html?msg=NeuroFedora+Meeti… The meeting will be chaired by @ankursinha. The agenda for the meeting is: - New introductions and roll call. - Tasks from last week's meeting (nothing here this time) - Open Pagure tickets: https://pagure.io/neuro-sig/NeuroFedora/issues?status=Open&tags=S%3A+Next+m… - CompNeuro lab compose status check. - Neuroscience query of the week. - Next meeting day, and chair. - Open floor. We hope to see you there! -- Thanks, Regards, Ankur Sinha "FranciscoD" (He / Him / His) | https://fedoraproject.org/wiki/User:Ankursinha Time zone: Europe/London

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FOSDEM 2021: February 6 and 7, online
by Ankur Sinha 03 Sep '20

03 Sep '20

Hello, Just a quick note that FOSDEM 2021 will be held online on February 6 and 7, 2021. https://fosdem.org/2021/news/2020-09-01-dates-fosdem-2021/ NeuroFedora was presented at the FOSDEM 2020 research track. You can see the complete schedule from 2020's sessions here and also listen to Aniket (@major)'s talk: https://archive.fosdem.org/2020/schedule/track/open_research_tools_and_tech… -- Thanks, Regards, Ankur Sinha "FranciscoD" (He / Him / His) | https://fedoraproject.org/wiki/User:Ankursinha Time zone: Europe/London

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Fwd: [Slicer] Integrating ITK and VTK: A Survey
by Morgan Hough 01 Sep '20

01 Sep '20

---------- Forwarded message --------- From: Jean Christophe Fillion Robin (Kitware) via 3D Slicer Community < slicer(a)discoursemail.com> Date: Tue, Sep 1, 2020 at 15:22 Subject: [Slicer] Integrating ITK and VTK: A Survey To: <morgan.hough(a)gmail.com> Dear 3D Slicer community, We need your input! We would like community feedback on our plans to create an enhanced version of the Visualization Toolkit (VTK) <https://vtk.org> that includes the image segmentation, registration and analysis capabilities of the Insight Toolkit (ITK) <https://itk.org>. This combination of popular open source packages would simplify research and development of scientific applications in C++, Python, and JavaScript. It would also bring extensive image analysis capabilities to ParaView and other VTK-based applications. If you are willing, we would greatly appreciate it if you would complete this 10 question survey: https://www.surveymonkey.com/r/WRPHW78 Please provide your feedback by *Tuesday, September 15, 5pm ET*. Background: VTK and ITK are already used together in many C++, Python, and JavaScript scientific applications such as 3D Slicer, Osirix, ParaView Glance, and ITKWidgets. These applications demonstrate the power of combining visualization and image analysis algorithms, particularly when building models from image data for simulations, applying interactive segmentation techniques, or visualizing image registration results. However, VTK and ITK use different data processing pipelines, use different coordinate systems, and support different data structures and file formats. These differences confound the development of integrated applications: inducing hard-to-find errors and requiring re-implementation of data conversion methods. As we formulate a plan to integrate ITK into VTK, we would like feedback from the community, so that our work is guided by their current and future needs and desires. Thank you and best regards, – Kitware Developers ------------------------------ Visit Topic <https://discourse.slicer.org/t/integrating-itk-and-vtk-a-survey/13285/1> or reply to this email to respond. To stop receiving emails about this topic, category, or all discussions, click here to unsubscribe <https://discourse.slicer.org/email/unsubscribe/c5da6565bf4b3beb3e973addb337…> .

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New NeuroFedora meeting time: please fill in the whenisgood
by Ankur Sinha 01 Sep '20

01 Sep '20

Hello, We're going to restart our public meetings in ~2 weeks. These meetings are open for everyone to attend, not just the NeuroFedora volunteers. Could everyone that would like to attend the meetings please fill in the whenisgood to indicate your preferences? http://whenisgood.net/bwsq9fd We'll look at the results and settle on a new time at the end of next week. -- Thanks, Regards, Ankur Sinha "FranciscoD" (He / Him / His) | https://fedoraproject.org/wiki/User:Ankursinha Time zone: Europe/London

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Neurofedora September 2020