Tag Archives: workflows

CUDDELing up to metabolomics in Hong Kong

- January 22, 2018

As mentioned in our Happy New Year blog post, one of the highlights in 2017 was a second GigaScience hackathon workshop which we held in November last year in our Hong Kong BGI office. Funding for this workshop came from a project we have called CUDDEL which was awarded a grant by the BBSRC from their China […]

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Guest posting: Conda as a new standard for Galaxy tool dependencies

- September 20, 2016

The Galaxy community is one that shares similar reproducibility goals with GigaScience, having a computational platform that allows users to share workflows, histories and wrapped computational tools in an easy-to-use and open source interface. Björn Grüning and The Intergalactic Utilities Commission of Galaxy have a guest posting here to announce new changes that will make development and presentation of tools and pipelines through Galaxy even more reproducible and usable.

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Open bioinformatics in the house of the mouse.

- July 10, 2016

The 2016 Bioinformatics Open Source Conference has just finished here at Disney World Orlando, and here is the write up of the meeting, with discussion on the merits of open bioinformatics and closed cartoons.

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Of Parasites & Protocols, Part 3. Author Q&A with Tony Papenfuss

- June 16, 2016

Following our announcement this month of a new collaboration and integration with protocols.io, we’ve gone into more detail on the first two papers that have utilised this open access repository of scientific methods and collaborative protocol-centered platform. To give some insight into his work, we have one of our author Q&As with Associate Professor Tony Papenfuss, lead author of our scabies genome paper.

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Reproducible Research Resources for Research(ing) Parasites

- June 3, 2016

Two new research papers on scabies and tapeworms published today showcase a new collaboration with protocols.io. This demonstrates a new way to share scientific methods that allows scientists to better repeat and build upon these complicated studies on difficult-to-study parasites. It also highlights a new means of writing all research papers with citable methods that can be updated over time.

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GigaMetabolomics Strikes Again: More BYO Data Parties and a Thematic Series

- March 13, 2016

The genomics community has been held up as an exemplar in data sharing practices since the human genome project, but the metabolomics community is catching up fast, with the Metabolights database being the fast growing repository at the EBI. In this light, GigaScience has been actively involved in reaching out and engaging with the metabolomics […]

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Getting Techy With It: GigaScience Technology Update 2014

- November 27, 2014

When it comes to technology, GigaScience has always been open and willing to embrace new ways of integrating technology in its publishing processes, with the ultimate goal of working towards more reproducible, interactive and executable papers. So far, 2014 has been an extremely busy year for Team Giga with regards to various technical developments as […]

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CARMEN, reproducible research and push-button papers

- March 26, 2014

Researchers release a treasure trove of data on the developing retina, pushing the boundaries of neuroscience publishing by presenting it dynamically and reproducibly. A new paper in GigaScience today demonstrates a major step forward for reproducible research and public data-sharing in the neurosciences with the publication and release of a huge cache of electrophysiology data […]

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Continuing our #usegalaxy series at the 2014 Galaxy Community Conference

- February 20, 2014

The upcoming 2014 Galaxy Community Conference (GCC2014) has just opened early registration, and following from our series announced at the last meeting we are renewing our call for papers for our special thematic focused series on studies utilizing large-scale datasets and workflows. For those not part of their large and rapidly growing user base, Galaxy is an open, web-based platform for data […]

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Rewarding Reproducibility: First Papers in our Galaxy Series utilizing our GigaGalaxy platform

- February 6, 2014

Push the button! GigaScience moves toward more interactive articles Research articles are being published with increasingly large and complicated supporting datasets, together with the software code used in analyses of the data. However, there is a growing number of studies reporting the inability to reproduce previously published findings which may, at least in part, be […]

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