federikovi

Google Summer of Code 2021 - Final Report

By Federica Trevisan ☀️

Hey there! I'm Federica, recent master's graduate in Data Science and participant of the Google Summer of Code '21. During the summer I worked with Wellcome Trust, which comes under the Open Bioinformatics Foundation, on the project entitled Developing WellcomeML further for the visualisation of academic research data under the guidance of my mentors: Antonio Campello, Elizabeth Gallagher and Jeff Uren. This is the final report regarding the past three months of GSoC summer.

Project synopsis

WellcomeML is a python package containing a set of utility functions that use machine learning for reading, processing, embedding and classifying academic text data like publications, grants, and other documents. The need for developing a new feature for expanding WellcomeML with further visualisation modules has emerged; in this specific case the objective is to

fomightez

This is a follow-up on an exchange started here. My extended reply follows...

Main use

Typically I am using the code that had been adapted from the templates into full-blown scripts to perform steps in the data analysis with the notebook as as way to perform the steps and document and package everything together.

Usually I am doing this with notebooks that either aren't ready to be shared, and so I just upload them to work on them as I develop an analysis.

joshkh

Thanks to Vivek for his great proposal! https://gist.github.com/vivekkrish/2e5e4128efbbf2014c194aae6b83d245

Assumptions:

• Dependencies are bundled into the app (requirejs, browserify, webpack)

Our justification is that sharing dependencies between third party tools introduces levels of complexity that are expensive (time consuming) and can be challenging to developers. If we find that third party apps are truly to large then we'll reconsider a more complicated approach.

App structure:

cybersiddhu

Aim

The idea was to have a intermine prototype for dictybase, dictymine running with a basic Genes -> GO -> GO annotation with all the basic features up and running. And then try out a deploy to google cloud using my stack of docker and kuberntes

Progress

• On the first day saw the new intermine UI redgenes which i set it up with a simple

hanowell

# Clear. Dat. Workspace.
rm(list = ls())

# Load. Dem. Packages.
library(tidyverse)

# Create. Dat. Data.
dat <- data.frame(category = LETTERS[1:4],
                  fraction = c(0, 20, 30, 50)) # Extra zero datapoint to keep hole in the donut.

Hendekagon

div::before {
  width: 3em;
  top: -2.6em;
  height: 3em;
  transform-origin: 50% 50%;
  transform: rotate(-29deg);
  position: relative;
  z-index: 10000000;
  margin-bottom: -3em;
  content: url("data:image/svg+xml;utf8,<svg height='100%' viewBox='-8 -8 16 16' width='100%' xmlns='http://www.w3.org/2000/svg'><g><rect fill='white' height='5' stroke-width='0.25' stroke='black' transform='rotate(45) translate(8,8)' width='5' x='-10.5' y='-10.5'></rect><rect fill='white' height='5' stroke-width='0.25' stroke='black' width='15' x='-7.5' y='0'></rect><text font-family='monospace' font-size='2.5' x='-5' y='3.25'>CHEESE</text></g></svg>");

jasongilman

Atom Clojure Setup

This describes how I setup Atom for an ideal Clojure development workflow. This fixes indentation on newlines, handles parentheses, etc. The keybinding settings for enter (in keymap.cson) are important to get proper newlines with indentation at the right level. There are other helpers in init.coffee and keymap.cson that are useful for cutting, copying, pasting, deleting, and indenting Lisp expressions.

Install Atom

Download Atom

The Atom documentation is excellent. It's highly worth reading the flight manual.

owenrh

;; this is not a windowed debounce, it is a paused debounce
;; (the timer is reset on each non-timer value)
(defn debounce [ms somefunc]
  (let [in (chan)
        out (chan)]
    ; debounce in channel - based on https://gist.github.com/scttnlsn/9744501
    (go-loop [last-val nil]
      (let [val (if (nil? last-val) (<! in) last-val)
            timer (timeout ms)
            [new-val ch] (alts! [in timer])]

joshkh

<!doctype html>
<html>
  <head>
    <script src="http://cdn.intermine.org/js/intermine/imjs/3.14.0/im.js"></script>
  </head>
  <body>
    
    <script>
      var flymine   = new imjs.Service({root: 'www.flymine.org/query'});
      var query     = {

danevans

(ns util.core
  (:import [goog Delay]))

(defn debounce [f interval]
  (let [timeout (atom nil)]
    (fn [& args]
      (when-not (nil? @timeout)
        (.disposeInternal @timeout))
      (reset! timeout (Delay. #(apply f args)))
      (.start @timeout interval))))