<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><span id="docs-internal-guid-9566dd95-7fff-aa86-5f4a-82dcfd3e598a" class=""><div style="text-align: left; line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 12pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">Dear all,</span></div><div style="text-align: left; line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 12pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">I am Sheriff, Project Leader at European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, UK.</span></div><div style="text-align: left; line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><font face="Arial" size="3" class=""><span style="white-space: pre-wrap;" class="">Jacob invited me to co-lead this subgroup and I gladly accepted it.</span></font></div><div style="text-align: left; line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><br class=""></div><div style="text-align: left; line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><font face="Arial" size="3" class=""><span style="white-space: pre-wrap;" class="">Please find below a brief description of our subgroup's focus and key issues we will try to address.</span></font></div><div style="text-align: left; line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><br class=""></div><div style="text-align: left; line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><font face="Arial" size="3" class=""><span style="white-space: pre-wrap;" class="">Btw, I am giving a talk on “Reproducibility of models” on January 21 (Thursday) at 3pm Eastern Standard Time</span></font></div><font face="Arial" size="3" class=""><span style="white-space: pre-wrap;" class=""><br class=""><a href="https://iu.zoom.us/meeting/register/tZYqd-2srD8tGtCXDem4Cka08rBz5fDW0EQR" class="">https://iu.zoom.us/meeting/register/tZYqd-2srD8tGtCXDem4Cka08rBz5fDW0EQR</a></span></font></span><div class=""><font face="Arial" size="3" class=""><span style="white-space: pre-wrap;" class=""><br class=""></span></font></div><div class=""><font face="Arial" size="3" class=""><span style="white-space: pre-wrap;" class=""><br class=""></span></font></div><div class=""><font face="Arial" size="3" class=""><span style="white-space: pre-wrap;" class="">I will talk about our recent work, where we analysed</span> <span style="white-space: pre-wrap;" class="">455 models from published articles and found that half of them could not be reproduced</span></font> </div><div class=""><font face="Arial" size="3" class=""><span style="white-space: pre-wrap;" class="">using the information provided in the manuscript. I will discuss the reasons why models often fail to reproduce and the solution we propose to tackle this during the peer-review process.</span></font></div><div class=""><font face="Arial" size="3" class=""><span style="white-space: pre-wrap;" class=""><br class=""></span></font></div><div class=""><font face="Arial" size="3" class=""><span style="white-space: pre-wrap;" class="">Full BioRxiv manuscript here</span></font></div><div class=""><a href="https://www.biorxiv.org/content/10.1101/2020.08.07.239855v1" style="color: rgb(149, 79, 114); font-family: Arial, sans-serif; font-size: 16px;" class="">https://www.biorxiv.org/content/10.1101/2020.08.07.239855v1</a></div><div class=""><font face="Arial" size="3" class=""><span style="white-space: pre-wrap;" class="">This is now accepted in Mol Sys Bio and I will present some more results.</span></font></div><div class=""><font face="Arial" size="3" class=""><span style="white-space: pre-wrap;" class=""><br class=""></span></font></div><div class=""><font face="Arial" size="3" class=""><span style="white-space: pre-wrap;" class=""><br class=""></span></font></div><div class=""><font face="Arial" size="3" class=""><span style="white-space: pre-wrap;" class="">I am Jacob had some initial discussion, we have some excellent plants for our groups activities. Hopefully we can meet soon and discuss them.</span></font></div><div class=""><font face="Arial" size="3" class=""><span style="white-space: pre-wrap;" class=""><br class=""></span></font></div><div class=""><font face="Arial" size="3" class=""><span style="white-space: pre-wrap;" class=""><br class=""></span></font></div><div class=""><font face="Arial" size="3" class=""><span style="white-space: pre-wrap;" class="">Best regards</span></font></div><div class=""><font face="Arial" size="3" class=""><span style="white-space: pre-wrap;" class="">Sheriff</span></font></div><div class=""><font face="Arial" size="3" class=""><span style="white-space: pre-wrap;" class=""><br class=""></span></font></div><div class=""><font face="Arial" size="3" class=""><span style="white-space: pre-wrap;" class=""><br class=""></span></font></div><div class=""><font face="Arial" size="3" class=""><span style="white-space: pre-wrap;" class=""><br class=""></span></font></div><div class=""><font face="Arial" size="3" class=""><span style="white-space: pre-wrap;" class=""><br class=""></span></font></div><div class=""><font face="Arial" size="3" class=""><span style="white-space: pre-wrap;" class=""><br class=""></span></font><span class=""><div style="text-align: left; line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><font face="Arial" size="3" class=""><span style="white-space: pre-wrap;" class=""><br class=""></span></font></div><div style="line-height: 1.38; text-align: center; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 12pt; font-family: Arial; font-weight: 700; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">MODEL REPRODUCIBILITY, CREDIBILITY AND STANDARDIZATION SUBGROUP</span></div><div style="line-height: 1.38; text-align: center; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-family: Arial; font-weight: 700; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">MSM WORKING GROUP ON MULTISCALE MODELING OF VIRAL PANDEMICS</span></div><br class=""><div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">Computational biological and medical models attempt to capture knowledge in a way that can be more easily shared than human language. The number of computational medical models are increasing. However, reuse of models is still rare indicating that there is still a gap that needs to be closed for computational models to become useful. Even published models are rarely reusable out of the box for multiple reasons. Many times the models just cannot be reproduced. </span></div><div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">One major reason is the lack of adoption of community standards by modellers despite many efforts. Model codes are either not-shared publicly or shared in non-standard formats, which makes it difficult to reuse and integrate models.</span></div><div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">In turn this causes disbelief of many stakeholders in credibility of models. This subgroup intends to explore these issues and recommend potential remedies. Those issues include:</span></div><div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">- Repeatability and Reproducibility of models in publications and repositories</span></div><div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">- Credibility of models</span></div><div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">- Standardization efforts & specifications for:</span></div><div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class=""> 1) Models and modeling technologies.</span></div><div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class=""> 2) Modeling data</span></div><div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">- Model annotation</span></div><br class=""><div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-family: Arial; font-weight: 700; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">Known specific issues:</span></div><ul style="margin-top: 0px; margin-bottom: 0px; padding-inline-start: 48px;" class=""><li dir="ltr" aria-level="1" style="list-style-type: disc; font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre;" class=""><div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">Models are written in different languages</span></div></li><li dir="ltr" aria-level="1" style="list-style-type: disc; font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre;" class=""><div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">Models require adaptation towards integration</span></div></li><li dir="ltr" aria-level="1" style="list-style-type: disc; font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre;" class=""><div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">Models are not licensed in an easy way that allows reuse</span></div></li><li dir="ltr" aria-level="1" style="list-style-type: disc; font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre;" class=""><div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">Models are hard to locate many times as those are published in different sources despite many repositories available</span></div></li></ul></span><div class=""><br class=""></div></div><br class=""><br class=""><div class="">
<div>-----------------------------------------------------------------------<br class="">Rahuman Sheriff PhD<br class="">Project Leader<br class="">European Bioinformatics Institute <br class="">European Molecular Biology Laboratory (EMBL-EBI)<br class="">Welcome Trust Genome Campus<br class="">Hinxton Cambridge CB10 1SD, UK<br class=""><a href="mailto:sheriff@ebi.ac.uk" class="">Email: sheriff@ebi.ac.uk</a><br class="">-----------------------------------------------------------------------</div><div class=""><br class=""></div><br class="Apple-interchange-newline">
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