[Fwd] COMBINE 2020: Registration open; Call for abstracts, breakouts and tutorials
by Ankur Sinha
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
3 years, 6 months
I want to be a part of NeuroFedora!
by Vivek Sharma
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
3 years, 7 months
Re: Orphaned packages looking for new maintainers
by Ankur Sinha
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
3 years, 7 months
Fwd: [Slicer] Integrating ITK and VTK: A Survey
by Morgan Hough
---------- 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
------------------------------
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3 years, 7 months
