bioinformatics-list October 2023

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Phylomania 2023: Like and subscribe!!
by Michael Charleston 13 Oct '23

13 Oct '23

Dear all, The registration page, payment page and a cheeky announcement about a (free!) Cogent3 workshop are all live on the Phylomania 2023 web page! Here it is in case Google can't find it for you: http://www.maths.utas.edu.au/phylomania/phylomania2023.html Can't wait to see you all! Michael Charleston [cid:b3651a8f-8aa0-4f81-8f66-598bae99e09e] Phylomania 2023: November 22-24 Specialty Chief Editor in Frontiers in Ecology and Evolution - Coevolution Mathematical Biology Group Professor in Bioinformatics School of Natural Sciences University of Tasmania AUSTRALIA Phone: +61 3 6226 2444 This email is confidential, and is for the intended recipient only. Access, disclosure, copying, distribution, or reliance on any of it by anyone outside the intended recipient organisation is prohibited and may be a criminal offence. Please delete if obtained in error and email confirmation to the sender. The views expressed in this email are not necessarily the views of the University of Tasmania, unless clearly intended otherwise.

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Fw: Cogent3 workshop at Phylomania announcement
by Michael Charleston 03 Oct '23

03 Oct '23

From: Gavin A Huttley <Gavin.Huttley(a)anu.edu.au> Sent: Tuesday, 3 October 2023 2:54 PM To: Michael Charleston <michael.charleston(a)utas.edu.au> Subject: Cogent3 workshop at Phylomania announcement Hi 👋! The development team of cogent3<https://protect-au.mimecast.com/s/RVN3C3Q870UpzOogZigneHc?domain=cogent3.org> will run a half-day Data Wrangling with Cogent3 Workshop on the afternoon of 21st November 2023. This is before the start of Phylomania, and it's free 🎉! You can register here<https://protect-au.mimecast.com/s/IM2TC4QZgDUBKqE2rUxaS9_?domain=forms.gle>. Read on past the signature to see workshop details. We hope you can join us! On behalf of the cogent3 developer team, Gavin Huttley ________________________________ Data Wrangling with Cogent3 The workshop is geared towards developers who specialize in phylogenetic methods. Acquiring empirical data for evaluating the performance of a new method is challenging. Your choice of data has important ramifications for your evaluation of the performance of your method. While the standard strategy of recycling published data sets is convenient, this risks perpetuating biases embedded in those data sets. We will show how cogent3<https://protect-au.mimecast.com/s/RVN3C3Q870UpzOogZigneHc?domain=cogent3.org> and associated tools can greatly simplify getting public data for analyses, serving the needs of phylogenetic method developers. As there is an overlap with standard phylogenetic data pre-processing workflows, users of phylogenetic (or molecular evolutionary) methods can also benefit from attending this workshop. Workshop Content The topics we will cover are: * Factors for method developers to consider when designing experiments. * How to extract specific types of sequences (e.g. by homology type, sequence class, or level of divergence) from biological databases like Genbank and Ensembl. * Handling inconsistencies in biological data resources. * Multiple sequence alignment and subsequent quality control. Prerequisites All you need for this workshop is a laptop and some familiarity with command-line applications. Ideally, you should be able to install software on your machine (see Computer Setup<https://protect-au.mimecast.com/s/UJQ0C5QZjEUZL23PAcywB7p?domain=github.com> on the wiki). More workshop information Details regarding physical location and setting up your computer before the workshop will be posted to the Cogent3 Workshop Wiki<https://protect-au.mimecast.com/s/Wuq5C6X1k7CrYq76Xf51HA3?domain=github.com>. We look forward to seeing you there! 👾 cogent3's development team. ________________________________ Professor Gavin Huttley, Research School of Biology, ANU College of Science, RN Robertson Building, 46 Sullivans Creek Road, The Australian National University Canberra ACT 2600 Australia +61 2 6125 5308 https://biology.anu.edu.au/research/groups/huttley-group-bioinformatics-mol…<https://protect-au.mimecast.com/s/5QBFC71Zl7fA1w2XLcqzgE7?domain=biology.an…> CRICOS #00120C ________________________________ This email is confidential, and is for the intended recipient only. Access, disclosure, copying, distribution, or reliance on any of it by anyone outside the intended recipient organisation is prohibited and may be a criminal offence. Please delete if obtained in error and email confirmation to the sender. The views expressed in this email are not necessarily the views of the University of Tasmania, unless clearly intended otherwise.

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bioinformatics-list October 2023