If you are a #Python developer and active in the #COBRA field, please voice your opinion on potential synergies generated by github.com/opencobra/cobr… #PythonDevelopers #PythonProgramming
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cobrapy
18 posts
cobrapy
@open_cobrapy
#metabolic #Modeling in #Python preferably with @sbmlnews
Katılım Mayıs 2018
3 Takip Edilen298 Takipçiler
@enit7677 @COBRAcon2020 @TheCOBRAToolbox @Nathan_E_Lewis @mherrgar @phantomas1234 @NCIEytanRuppin That's a pretty cool idea! We put a similar idea into an application to @cziscience. We should hear back from that by the end of the month so maybe that idea could be built upon.
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@COBRAcon2020, @TheCOBRAToolbox , @open_cobrapy, w/ the 🐍 conference canceled, could we organize a (semi-)regular online seminar series? any other format? @Nathan_E_Lewis, @mherrgar, @phantomas1234, @NCIEytanRuppin and many, many more ...
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We want to make getting help for cobrapy easier! If you dislike mailing lists as much as we do, cast your vote on where to ask questions: #Bioinformatics @StackExchange (bioinformatics.stackexchange.com) or #Biostars (biostars.org). Poll here dudle.inf.tu-dresden.de/cobra-help-pla…
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We are trying to make the cobrapy community more inclusive. We will add a code of conduct and are looking for members to join the committee that handles complaints. Get involved, no coding required! Hopefully the easiest job you ever took on 😉
DM or github.com/opencobra/cobr…
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cobrapy retweetledi
results now on #BioRxiv at biorxiv.org/content/10.110…
feedback welcome!
Maureen Carey@MaureenACarey
hey #cobra users- @papinsysbio, @jtyurkovich, & I made a short poll to survey the field on #cobra standards & resources to build on the conversations @ @COBRAcon2018 please add your perspective & share w/ colleagues & collaborators! poll linked here: goo.gl/forms/9a37gKUH…
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cobrapy retweetledi
A new class of random sampler for COBRA models: biorxiv.org/content/10.110…. Uniform coverage on difficult and non-convex models. Compatible with @TheCOBRAToolbox and @open_cobrapy. Available at github.com/jensenlab/gaps….
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@ctseto @DynamicWebPaige @GoogleColab @TensorFlow Would it be beneficial to provide an 'official' Docker image with cobrapy for this?
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Being able to launch a @GoogleColab notebook directly from the @TensorFlow documentation: priceless. 😁✨
Farza 🇵🇰🇺🇸@FarzaTV
Literally everything in the Tensorflow docs now comes with a Docker container ready to run stuff. No more stupid python, conda, virtualenv, or cuda errors. The time it takes to go from docs -> running a model on a GPU is now two minutes. BEAUTIFUL.
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We just released version 0.15.0 which includes a major revision of the SBML parser by @konigmatt. Also SBML groups by @medlockgreg and convenient configuration by @synchon_mandal. Check it out directly with `pip install -U cobra` pypi.org/project/cobra/ and share your experience.
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Help shape model encoding and how models can be built in #cobrapy in future.
Maureen Carey@MaureenACarey
just a reminder to all #cobra users to participate in our survey on standards and resources to follow up on our discussion at @COBRAcon2018 thanks for your participation!
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Dear community, most voters so far favor Python 3 and dropping support for Python 2, do you agree? Let us know until Friday 18 in our #cobrapy user survey goo.gl/forms/sZzT737i…
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@ctseto @KevinBlighe It's a matter of incentivization, there are few opportunities where decent software development and maintenance are possible. It's not a state of affairs that I support but I can also see how many academic groups simply have nothing to gain after publishing.
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@KevinBlighe Some processes are continuously monitored...like @open_cobrapy . older subpackages like, say, mCADRE, peak and diminish, instead superseded by better pipelines. Instead of upgrading the truck, new vehicles every time!
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Please join our second user survey goo.gl/forms/bv88ceTI… on the state of Python 2 and how to improve help channels.
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@ad_am_ara Most issues we see come from handling Python and the linear programming solvers. After that it's `pip install cobra`. 🐍 Happy to help your students or accept PRs for better installation docs 😉
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When you suggested to the new student to install COBRA @open_cobrapy
Evan Kirstel #B2B #TechFluencer@EvanKirstel
Worst #techsupport issue ever
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Curious about latest developments around #cobrapy? Interested in reading about the experience of contributing to open source tools? Our @gsoc student @synchon_mandal blogs about all his latest work @synchon_mandal" target="_blank" rel="nofollow noopener">medium.com/@synchon_mandal
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In tonight's release 0.13.0, we see backward incompatible additions for specific access to boundary reactions and the ability to compute minimal media! Thank you @thaasophobia Find out more at github.com/opencobra/cobr…
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Just released version 0.12.1 which enables full capabilities for Gurobi, better non-optimal solution inspection, and improved summary functions plus numerous fixes. Read more on GitHub github.com/opencobra/cobr…
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Just out: First user survey of 2018! goo.gl/forms/RcFtqlRe… Help us prioritize our efforts. #Python #Metabolic #Modeling And more awesomeness: 0.12.0 release adds ROOM and geometric FBA thanks to @synchon_mandal 🎉
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