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Displaying posts with the tag: data [Clear Filter]

Pre-trained Machine Learning Models for Developmental Biology

Posted by on October 29th, 2019

Pre-trained Models for Developmental Biology Authors: Bradly Alicea, Richard Gordon, Abraham Kohrmann, Jesse Parent, Vinay Varma Our virtual discussion group (DevoWormML) has been exploring a number of topics related to the use of pre-trained models in machine learning (specifically deep learning). Pre-trained models such as GPT-2 [1], pix2pix [2], and OpenPose [3] are used for[…]

EmbryoPhenomics: An open-source technological platform

Posted by on February 5th, 2019

Tills O, Spicer JI, Grimmer A, Marini S, Jie VW, Tully E, Rundle SD. 2018. A high-throughput and open-source platform for embryo phenomics. PLOS Biology, 16:1-19. https://doi.org/10.1371/journal.pbio.3000074 Background A seasoned graduate student gave me some valuable advice at the outset of my PhD. She told me to FIND A BETTER WAY!  We were both working on[…]

Showing distributions

Posted by on August 6th, 2018

When reading about co-evolution of prey and predators, I stumbled across a cute new plot type: a half boxplot, half dot plot to show data distributions.     Wilson used this plot to simultaneously visualize summaries about their data (center, spread) and the actual data points. This allows us, the audience, to learn a lot[…]

New embryo phenotype data from the DMDD programme

Posted by on June 15th, 2018

Following our latest data release, the DMDD website (dmdd.org.uk) now contains detailed phenotype data for nearly 700 embryos from 82 different knockout mouse lines. Highlights include the identification of limb defects and cysts in Col4a2 knockouts and replication of the major features of Meckel syndrome in B9d2 knockouts. We have begun to add immunohistochemistry image[…]

New resources section on the Node

Posted by on November 23rd, 2017

Since its launch in 2010, the Node has functioned as a community resource for developmental biologists. When I started my 3 month internship in September (see my introductory post here), we decided to utilise my experience as an active researcher to redesign and update the Node’s resources page. This included transferring the resources from the[…]

9.5 million knockout mouse embryo images now available

Posted by on July 20th, 2017

A new set of DMDD embryo and placenta data has been released, taking our total dataset to 9.5 million images of around 1300 embryos. DMDD is a primary screen of embryonic lethal knockout mice, and all data can be freely accessed at dmdd.org.uk. Detailed phenotypes are available for embryos from 73 different knockout lines, and[…]

Leaving the bar in five steps

Posted by on March 24th, 2017

Introduction Graphs (or charts or plots) are often used for the display and summary of data. They are essential tools for the communication of results in presentations or manuscripts. One particular type of graph, the bar graph, is often used to quantitatively compare (multiple) conditions. The earliest known example of a bar graph, dates from[…]

New phenotype dataset available for embryonic-lethal mouse knockouts

Posted by on December 1st, 2016

    This post originally appeared on Annotations, the DMDD blog.   New image and phenotype data for embryos and placentas from embryonic lethal knockout mouse lines has been made available on the DMDD website today. The knockout data includes the ciliary gene Rpgrip1l as well as Atg16l1, a gene encoding a protein that forms[…]

New DMDD embryonic-lethal mouse data now available

Posted by on August 15th, 2016

  This post was originally posted on the DMDD blog.   New embryonic-lethal knockout mouse lines are now available on the DMDD database. If you haven’t previously taken a look at our data (or even if you have) now would be a good time to explore our website.  We’ve added new embryo phenotype data and[…]

Of mice and men: exploring Mouse ENCODE

Posted by on December 17th, 2014

The Mouse ENCODE Project released a slew of papers late last month reporting findings from a three-year effort to comprehensively map functional elements in the mouse genome. Their major findings are summarized in an integrative paper in Nature (Yue, F. et. al., 2014). Similar to the goals of the human ENCODE project (The ENCODE Project Consortium,[…]