@rsmsheriff

Senior Project Leader, BioModels, EMBL-EBI

 Cambridge, England
Joined July 2017
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  • Following73
  • Followers108
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New version of SimBio is out github.com/orgs/dyscolab/dis… To learn about SimBio read our manuscript doi.org/10.1093/bioinformati…

Version 1.1.0 · dyscolab · Discussion #4

Version 1.1.0 Symbolite, poincare and simbio have released version 1.1.0, wich includes two major features: Generation of model reports in LaTeX. Stochastic simulations with Gillespie's algorit...

github.com
Oliverio starosta@StOliverioApr 10
A month ago we released version 1.0 of Poincare and SimBio, python libraries for simulating dynamical systems and chemical reactions. We now released version 1.1 with: - Reports with a system's equations and variables in Latex. - Stochastic simulation with Gillespie's algorithm.
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FROG analysis is an impactful advancement for improving reproducibility and reliability in the rapidly growing field of GEM modelling. Proud to share this exciting work after a 3-year journey. A huge thank you to all core team members and contributors! doi.org/10.1101/2024.09.24.6…
biomodels@biomodels27 Sep 2024
🎉 Excited to share our preprint on FROG analysis ensuring reproducibility, reusability and reliability of Genome-Scale Metabolic Models! It is a true community effort, kudos to 90+ co-authors! More details here: biorxiv.org/content/10.1101/… #Reproducibility #SystemsBiology #GEM

FROG Analysis Ensures the Reproducibility of Genome Scale Metabolic Models

Genome-scale metabolic models (GEMs) and other constraint-based models (CBMs) play a pivotal role in understanding biological phenotypes and advancing research in areas like metabolic engineering,...

biorxiv.org
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Rahuman Sheriff retweeted
biomodels@biomodels21 May 2024
Join Us for the remote BioModels ML Hackathon – June 20-21, 2024 dedicated to making machine learning models in life sciences FAIR and reproducible. Registration: tinyurl.com/FAIR-AIML-2024
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biomodels@biomodels27 Feb 2024
🌟 Our article on the Model of the Year 2023 is out! Check out the winners' innovative work in #FrontiersinSystemsBiology: doi.org/10.3389/fsysb.2024.1… 🏆 Dreaming of having your model in the spotlight? ☀️ Apply now for MOY2024 ebi.ac.uk/biomodels/competit… ⌛️Deadline: 29th Feb 2024!
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🚀 Launching "Poincaré & SimBio": Pure Python packages for modeling dynamic system 🔥Easy Python integration & extension 🔥SBML support 🔥Numba JIT compilation 4 top performance 🔥Python syntax for IDE-based error-detection, code analysis & refactoring 🔗 doi.org/10.1101/2024.01.10.5…
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Rahuman Sheriff retweeted
biomodels@biomodels18 Oct 2023
We were excited to announce the winners of the #modeloftheyear2023 competition at @icsb2023 Hartford, CT. Congratulations to the winners! A big shout-out to all participants who submitted their interesting models! Application for #MOY2024 is open! ebi.ac.uk/biomodels/competit…
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biomodels@biomodels12 Sep 2023
We are organizing the virtual @EBItraining course Mathematics of Life 2024 Join us for an introduction and hands-on training on modelling approaches, tools, and resources used in #systemsbiology Deadline: 26 November ebi.ac.uk/training/events/ma…
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ALERT! ELIXIR Machine Learning Focus Group & others are seeking industrial and academic partnerships for the following call: "Maximising the potential of #SyntheticData generation in healthcare applications" shorturl.at/fJSV0. Reach out to us if you are interested!
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A free public collection of #ArtificialIntelligence #machinelearning #models will greatly advance life science and medicine! With this grand vision in mind, we started our pilot effort to make AIML models #FAIR and #reproducible by extending @biomodels! biorxiv.org/content/10.1101/…

BioModelsML: Building a FAIR and reproducible collection of machine learning models in life...

Machine learning (ML) models are widely used in life sciences and medicine; however, they are scattered across various platforms and there are several challenges that hinder their accessibility,...

biorxiv.org
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Rahuman Sheriff retweeted
biomodels@biomodels7 Apr 2023
Did you know that you can not only submit models you authored but also curate published models and submit them to BioModels? Pedro Mendes @gepasi curated and submitted the vonDassow2000 model ebi.ac.uk/biomodels/MODEL230… Community curation is a great way to enhance public resources!
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Did you know that you can easily find, access and reuse, interoperable #systemsbiology models @biomodels? Join our #bioinformatics #webinar next week to find out more. Registration free but essential - ebi.ac.uk/training/events/ex… #mathematicalmodeling #computationalbiology
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Rahuman Sheriff retweeted
biomodels@biomodels9 Jan 2023
The deadline extended until 20th Jan 2023 to accommodate requests from our users and collaborators. Don't miss the opportunity to submit your application to enter the Model of the year 2023 competition!!!
biomodels@biomodels29 Nov 2022
To enter the competition, submit your model code in any format (e.g. SBML, CellML, Matlab, Python, C++, R, Julia scripts etc) and a brief summary highlighting its scientific outcome, novelty and impact. Deadline approaching soon (31/12/22). Cash prize and recognization awaiting!
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Rahuman Sheriff retweeted
EMBL-EBI@emblebi16 Nov 2022
📣Calling all early-career researchers who develop systems biology models! Our @biomodels colleagues have launched the first edition of their ‘Model of the year’ competition. Check out the entry requirements and submit yours for a chance to win! 🏆 ebi.ac.uk/about/news/updates…

BioModels competition: Showcase your model of the year

Competition celebrates importance of robust theoretical modelling for systems biology

ebi.ac.uk
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Just one week left. Apply Soon. Get hands-on experience to use several systems biology modelling tools and listen to lectures from experts in academia and the pharmaceutical industry. This beginners course is open to experimental biologists, bioinformaticians and mathematicians.
EMBL-EBI Training@EBItraining24 Jun 2022
We're going virtual! You can now join our #mathematicalmodelling course from anywhere in the world. We've reopened applications until 22 July if you would like your chance to join us and @AMartinezArias, @dr_drae, @rsmsheriff, @tomashelikar & co. 🔗ebi.ac.uk/training/events/ma…
EMBL-EBI Course. Mathematics of life: modelling molecular mechanisms. 12 - 16 September 2022. Virtual. EMBL-EBI logo.

ALT EMBL-EBI Course. Mathematics of life: modelling molecular mechanisms. 12 - 16 September 2022. Virtual. EMBL-EBI logo.

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We encoded 24 covid19 transmission models in highly interoperable SBML @sbmlnews using @COPASI_software as proof of concept. We discuss in our manuscript the advantage of using systems biology community standard to encode COVID19 models.
biomodels@biomodels27 Jun 2022
The early phase of #COVID19 pandemics exposed the difficulty in finding, accessing, reproducing and reusing #diseasetransmission models. To make COVID19 models #FAIR & #reproducible we recommend adoption of Systems Biology community standards for modeling preprints.org/manuscript/202…

FAIR Sharing of Reproducible Models of Epidemic and Pandemic Forecast

A major challenge for the dissemination, replication, and reuse of epidemiological forecasting studies during COVID-19 pandemics is the lack of clear guidelines and platforms to exchange models in a...

preprints.org
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Our paper on human immune digital twin is out. This is a first step towards a grand vision we are working towards!!! nature.com/articles/s41746-0…
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Job opening for Bioinformatician (Pandemic Preparedness) position at EMBL-EBI. More details here embl.org/jobs/position/EBI02…
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Let’s us work together as a community to improve reproducibility and curation of constraint-based models using #FROG community standard.
biomodels@biomodels25 Mar 2022
Hurray! We started to curate #constraint_based_models such as genome-scale metabolic models using #FROG, a @combine_coord standard developed over the past 2 years. Help us to reproduce your models and contribute to our community manuscript. More info at ebi.ac.uk/biomodels/curation…
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Rahuman Sheriff retweeted
biomodels@biomodels28 Jan 2022
Do you use or intend to use spatial multi-cellular models in your research? If yes, please complete this short survey docs.google.com/forms/d/e/1F… We propose to support curation, discoverability, reproducibility & archiving of multicellular spatial models of tissues in BioModels.
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Rahuman Sheriff retweeted
biomodels@biomodels24 Jan 2022
Shoutout to @suruchi_bakshi for setting great example to promote model #reproducibility. While curating her model we found a couple of mistakes in the manuscript. When reported, she not just clarified, but also went on to publish a correction of manuscript ebi.ac.uk/biomodels/BIOMD000…
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