Created Dockerfile

586458f1 · Stefan Eirich · 3657b0f8 · 586458f1 · 586458f1 · 3657b0f8
Verified Commit 586458f1 authored 5 years ago by Stefan Eirich
--- a/Dockerfile
+++ b/Dockerfile
+FROM jekyll/jekyll
+
+COPY . .
+
+CMD cp letter/index.md . && jekyll build
--- a/LICENSE
+++ b/LICENSE
+The MIT License (MIT)
+
+Copyright (c) 2015 Benjamin L. Moore
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
--- a/README.md
+++ b/README.md
-# Docker CV
-
--- a/_config.yml
+++ b/_config.yml
+markdown:   kramdown
\ No newline at end of file
--- a/_layouts/cv.html
+++ b/_layouts/cv.html
+<!doctype html>
+<html>
+<head>
+  <meta charset=utf-8 />
+  <title> Ben Moore's CV</title>
+  <link href="media/cv-screen.css" type="text/css" rel="stylesheet" media="screen">
+  <link href="media/cv-print.css" type="text/css" rel="stylesheet" media="print">
+  <link href="media/academicons.min.css" rel="stylesheet">
+
+  <!-- imports -->
+  <link rel="stylesheet" href="//maxcdn.bootstrapcdn.com/font-awesome/4.3.0/css/font-awesome.min.css">
+  <link href='http://fonts.googleapis.com/css?family=Open+Sans:400,300,700' rel='stylesheet' type='text/css'>
+</head>
+<body>
+  <div id="main">
+    <div id="content">
+    {{ content }}
+    </div>
+  </div>
+
+  <div class="footer"></div>
+
+</body>
+</html>
--- a/fonts/academicons.eot
+++ b/fonts/academicons.eot
--- a/fonts/academicons.svg
+++ b/fonts/academicons.svg
--- a/fonts/academicons.ttf
+++ b/fonts/academicons.ttf
--- a/fonts/academicons.woff
+++ b/fonts/academicons.woff
--- a/index.md
+++ b/index.md
+---
+layout: cv
+title: Ben Moore's CV
+---
+# Benjamin L. Moore
+Bioinformatics PhD and data scientist
+
+<div id="webaddress">
+<a href="mailto:ben@blm.io">ben@blm.io</a>
+|
+<i class="fa fa-github"></i> <a href="http://github.com/blmoore">blmoore</a>
+|
+<i class="fa fa-twitter"></i> <a href="http://twitter.com/benjaminlmoore">benjaminlmoore</a>
+</div>
+
+
+## Currently
+
+I'm a Bioinformatics Scientist at [Illumina](http://www.illumina.com/), based at their R&D site near Cambridge, UK. Here I develop software and use data science, machine learning and statistical programming to analyse large volumes of high-throughput sequencing data.
+
+## Employment
+
+`2015-` 
+__Illumina, Inc.__ Bioinformatics scientist (data scientist and statistical programmer)
+
+## Education
+
+`2012-15`
+__University of Edinburgh__ Bioinformatics PhD (supervisors: Colin Semple and Stuart Aitken). My thesis was titled _Unravelling higher order chromatin organisation through statistical analysis_ and is available through the [Edinburgh Research Archive](https://www.era.lib.ed.ac.uk/handle/1842/22906).
+
+`2011-12`
+__Imperial College London__ MSc Bioinformatics and Theoretical Systems Biology (_Distinction_)
+
+`2008-11`
+__University of York__ BSc Biology (_First class honours_)
+
+## Presentations
+
+### Tutorials
+
+`2014`
+WikiProject Computational Biology half-day tutorial (_ISMB_, Boston, USA)
+
+### Talks
+
+`2015`
+EdinbR: The Edinburgh R usergroup (_various_)
+
+MRC IGMM research seminars and section meetings (_various_)
+
+`2014`
+Unravelling higher order chromatin structure (_4<sup>th</sup> Edinburgh Bioinformatics meeting_, Edinburgh, UK)
+
+blogR: pop data analysis and R for the web (_Psychology R-users_, Edinburgh, UK)
+
+### Posters
+
+`2015`
+_Keystone Epigenomics_ (Keystone CO, USA)
+
+`2014`
+_ISMB_ (Boston MA, USA)
+
+_Genome informatics_ (Cambridge, UK)
+
+_Chromatin: From nucleosomes to chromosomes_ (Cambridge, UK)
+
+`2013`
+_Genome informatics_ (CSHL NY, USA)
+
+_EpiGeneSys_ (Cambridge, UK)
+
+
+## Publications
+
+<!-- ### Journals -->
+`2017`
+Peluso S, Douglas A, Hill A, De Angelis C, __Moore BL__ _et al._ Fibroblast growth factors (FGFs) prime the limb specific Shh enhancer for chromatin changes that balance histone acetylation mediated by E26 transformation-specific (ETS) factors. _eLife_, 6: e28590.
+
+Eberle MA, Fritzilas E, Krusche P, Källberg M, __Moore BL__ _et al._ A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree. _Genome Research_, 27:157-164.
+
+`2016`
+Yu N, Nützmann H-W, MacDonald JT, __Moore B__ _et al._ Delineation of metabolic gene clusters in plant genomes by chromatin signatures. _Nucleic Acids Research_, 44(5):2255-2265.
+
+`2015`
+__Moore BL__ _et al._ Integrative modeling reveals the principles of multi-scale chromatin boundary formation in human nuclear organization. _Genome Biology_, 16:110.
+
+Fraser J, Ferrai C, Chiariello AM, Schueler M, Rito T, Laudanno G, Barbieri M, __Moore BL__ _et al._ Hierarchical folding and reorganization of chromosomes are linked to transcriptional changes in cellular differentiation. _Molecular systems biology_, 11:852.
+
+`2013`
+__Moore BL__ _et al._ High–quality protein backbone reconstruction from alpha carbons using Gaussian mixture models. _Journal of computational chemisty_, 34(22):1881-9.
+
+`2011`
+Gardner PP, Daub J, Tate J, __Moore BL__ _et al._ Rfam: Wikipedia, clans and the “decimal” release. _Nucleic acids research_, 39(S1):D141-5.
+
+## Non-academic
+
+`2014` Pieces in _The Huffington Post_ (US): Here Are the Most Overrated and Underrated Movies of All Time; Celebrity Twitter Followers, by Gender ([huffingtonpost.com/benjamin-moore](http://www.huffingtonpost.com/benjamin-moore/))
+
+`2006–` Articles for _English Wikipedia_: European Nucleotide Archive, RNA thermometer, Toxin-antitoxin system and more ([en.wikipedia.org/wiki/User:Ben_Moore](https://en.wikipedia.org/wiki/User:Ben_Moore)).
+
+## Technical skills
+
+* R
+* Python
+* Javascript (incl. Typescript, Angular)
+* Go
+* HTML and CSS
+* LaTeX
+* Bash
+* Git / Mercurial
+* UNIX
+* Cluster computing
+* Docker
+* AWS
+
+## Areas of expertise
+
+* Bioinformatics
+* Statistics
+* Machine learning
+* Data visualisation
+* Software development
+* NGS and variant calling
+
+## Projects
+
+### github
+
+My [personal github account](https://github.com/blmoore) hosts my hobby development projects as well as listing contributions to open source tools. Examples include: shiny apps [blackspot](https://github.com/blmoore/blackspot) and [shinybrot](https://github.com/blmoore/shinybrot), as well as an R package hosted by CRAN ([mandelbrot](https://github.com/blmoore/mandelbrot)).
+
+### blog
+
+I write a data science blog at [blm.io](http://blm.io/blog) where I apply R and Python to open datasets and write-up the results. My posts have been featured by sites including FiveThirtyEight, BuzzFeed, AVclub, io9 and more, and also led to being an invited blogger at the Huffington Post. My original wordpress blog ([benjaminlmoore.wordpress.com](http://benjaminlmoore.wordpress.com)) has received over 150,000 unique visitors from 180 countries.
+
+### EdinbR
+
+I co-founded a usergroup for the R programming language in Edinburgh called EdinbR. I helped to organise our monthly meetings and built our website: [edinbr.org](http://edinbr.org). Our meetings attract 30-50 statisticians, data scientists and developers for talks and discussion about the R language and its applications. We're sponsored by Revolution Analytics and have an organisational github account at [github.com/EdinbR](https://github.com/EdinbR).
+
+### datarea
+
+I entered Imperial College's [Summer Data Challenge](https://www.imperial.ac.uk/data-science/education/summer-data-challenge/) competition, where entrants analysed a given dataset and then proposed a startup idea based on their results. I developed a modelling technique to select housing areas for investment and was awarded third place: £2,000 and startup support from Imperial Create Lab. My entry can be seen at [blm.io/datarea](http://blm.io/datarea) and the code is shared on my github account.
+
+## Awards
+
+MRC Capacity building scholarship (PhD fees + enhanced stipend)
+
+MRC Full postgraduate scholarship (MSc fees + stipend)
+
+ISCB computational biology Wikipedia competition 2013 ([doi:10.1371/journal.pcbi.1003242](http://dx.doi.org/10.1371/journal.pcbi.1003242); 2nd place)
+
+Imperial Create Lab's "Summer data challenge" ([summerdatachallenge.com](http://summerdatachallenge.com); 3rd place)
+
+Individual engagement grant from the Wikimedia Foundation to attend ISMB 2014
+
+Training accreditation for Wikimedia UK, the national chapter of the Wikimedia Foundation
+
+Front cover design selected for J. Comp. Chem. (34:22) ([doi:10.1002/jcc.23388](http://dx.doi.org/10.1002/jcc.23388))
+
+## Placements
+
+`2010-11`
+__Wellcome Trust Sanger Institute__ (_Cambridge, UK_)
+Worked for two summers on the Rfam database ([rfam.xfam.org](http://rfam.xfam.org)) in the Bateman group
+
+
+## Links
+
+<!-- fa are fontawesome, ai are academicons -->
+* <i class="fa fa-envelope"></i> <a href="mailto:ben@blm.io">ben@blm.io</a><br />
+* <i class="fa fa-github"></i> <a href="http://github.com/blmoore">blmoore</a><br />
+* <i class="fa fa-twitter"></i> <a href="http://twitter.com/benjaminlmoore">benjaminlmoore</a><br />
+* <i class="fa fa-linkedin"></i> <a href="https://www.linkedin.com/in/blmoore/">LinkedIn</a>
+* <i class="fa fa-stack-overflow"></i> <a href="http://stackoverflow.com/users/1274516/blmoore">StackOverflow</a>
+* <i class="fa fa-wikipedia"></i> <a href="https://en.wikipedia.org/wiki/User:Ben_Moore">Wikipedia Userpage</a><br />
+* <i class="ai ai-google-scholar"></i> <a href="http://scholar.google.com/citations?user=YMxsGpsAAAAJ">Google scholar</a>
+* <i class="ai ai-orcid"></i> <a href="https://orcid.org/0000-0002-4074-1933">ORCiD</a>
+* <i class="ai ai-figshare"></i> <a href="https://figshare.com/authors/Benjamin_Moore/99461">figshare</a>
+
+## References
+
+Available on request.
+
+<!-- ### Footer
+
+Last updated: May 2013 -->
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+
+
+ul {
+	position: relative;
+	left: 25%;
+	width: 65%;
+	margin-bottom: 1.5em;
+	margin-top: 1em;
+  columns: 3;
+  -webkit-columns: 3;
+  -moz-columns: 3;
+}
+
+
+li {
+	/* empty */
+}
+
+li ul {
+	position: relative;
+	left: 0;
+/*	margin-top: 0.25em; */
+}
+
+h1,h2,h3,h4 {
+	font-weight: 400;
+	font-family: Cousine,Verdana,sans-serif;
+	width: 65%;
+}
+
+h1 {
+	color: #fd9544;
+	text-align: left;
+	font-size: 3em;
+	line-height: 1em;
+	position: relative;
+	margin-top: 2em;
+	left: 25%;
+	/* padding: .1rem 1rem; */
+  text-shadow: 1px 1px #fff,
+      					1px 2px #ccc;
+}
+
+h1+p {
+	/*subtitle*/
+	color: #1D49A0;
+	font-style: italic;
+	font-size: 110%;
+	line-height: 2em;
+	margin-top: 0.5em;
+	margin-bottom: 0em !important;
+}
+
+h2 {
+	font-size: 1.1em;
+	/* color: #a00; */
+	color: #1D49A0;
+	margin-top: 2em;
+	position: relative;
+	top: 1.4em;
+	text-align: right;
+	width: 15%;
+}
+
+h3 {
+	color: #F07415;
+	font-size: 1em;
+	line-height: 2em;
+	position: relative;
+	top: 1.7em;
+	text-align: right;
+	width: 15%;
+}
+
+a {
+	color: inherit;
+	/*text-decoration:none*/
+}
+
+a:hover {
+	color:#39f
+}
+
+#webaddress {
+	margin-top: 0em;
+	position: relative;
+  margin-left: 25%;
+	color: #aaa;
+	font-family: Menlo,monospace,sans-serif;
+	font-size: 80%;
+}
+
+#webaddress a {
+	text-decoration: none;
+}
+
+em {
+	/*font-weight: bold; */
+	font-style: italic;
+}
+
+strong {
+	font-weight: bold;
+}
+
+#address {
+	display: none;
+}
+
+.footer {
+    -webkit-column-count: 3; /* Chrome, Safari, Opera */
+    -moz-column-count: 3; /* Firefox */
+    column-count: 3;
+		position: relative;
+		left: 25%;
+		margin-top: 2em;
+		margin-bottom: 7em;
+		margin-right: 0;
+		width: 65%;
+}
+
+#technical
+
+/*
+@media only screen and (max-width: 480px) {
+	make one column somehow...
+}*/