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Dave Lunt
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Evolutionary biologist, Academic, Researcher, Teacher
Evolutionary biologist, Academic, Researcher, Teacher

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New EvoPhylo blog post where I talk (on and on) about ReproPhylo our open phylogenomics environment   #phylogenetics   #python   http://hulluni-bioinformatics.github.io/ReproPhylo/

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Our ReproPhylo preprint is now on BioRxiv - we'd welcome suggestions and comments. Work by +Amir Szitenberg and +Max John. The website is here http://hulluni-bioinformatics.github.io/ReproPhylo/ #reproducibility  

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Work carried out by +Amir Szitenberg in my lab. We're hoping to have a preprint out this week and the GitHub repository is already up of course http://hulluni-bioinformatics.github.io/ReproPhylo/
ReproPhylo - a #phylogenomic analysis environment developed to ensure experimental reproducibility, to facilitate the handling of large-scale data, and to assist methodological experimentation.

http://figshare.com/articles/ReproPhylo_an_environment_for_reproducible_phylogenomics/1409426
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A new office decoration, a Sanger DNA sequencing gel film. It immediately provoked a conversation with an undergraduate tutee about the development of sequencing technology over time. Job done.
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My ReproPhylo: reproducible phylogenomics talk from +Nick Loman's  Balti and Bioinformatics Hangout

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We've made some improvements to sharing. You now can share papers directly on Google Plus, Twitter and Facebook. 

Also we added new keyboard shortcuts for sharing and improved subject lines for sharing emails. 

All the details on our blog:

https://paperpile.com/blog/share-science-on-twitter/

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A great discussion of Pinker's new book and scientific writing. Don't be misled Joan Strassmann LOVES it.

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I'm doing a short hangout on the 21st Jan as part of the #baltiandbioinformatics  series of bioinformatics meetings. Here's the link https://plus.google.com/events/cbtuikle0h2619obgjrgfu74424

The theme is "open data and reproducible bioinformatics". I'm going to talk about reproducible phylogenomics, and cover some of the issues we've addressed trying to modernise our way of dealing with phylogenomic data. +Amir Szitenberg and I have built ReproPhylo, a reproducible phylogenomics environment, as our solution. I really need to find time to blog about it but here are the #ReproPhylo links.
webpage: hulluni-bioinformatics.github.io/ReproPhylo/ documentation: http://goo.gl/yW6J1J

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Lets give stars for how well you share your #phylogenetic data! The idea comes from Tim Berners-Lee, but could work well for open phylo data. The answer? Its like a bag of chips/crisps. Personally I would like the list to start at zero stars because thats how computers count and it seems more fitting for not openly sharing to get no stars at all.

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Next in my series on reproducible #phylogenetics. Here I look at existing software that could be used reproducibly.
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