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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<html>
<head>
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<title>OpenLabNotebook</title>
<link type="text/css" rel="stylesheet" href="appbase.css">
</head>
<body class="wikidpad">
<span class="wikidpad parent-nodes">parent nodes: <br class="wikidpad" /><br class="wikidpad" /></span>
<a name=".h0" class="wikidpad"></a><h2 class="wikidpad heading-level2">V. Senderov's Phd Thesis Open Lab Notebook</h2>
<a name=".h47" class="wikidpad"></a><h3 class="wikidpad heading-level3">Todos</h3>
<span class="wikidpad todo">todo: import links from google docs</span><br class="wikidpad" />
<span class="wikidpad todo">todo: research open science</span><br class="wikidpad" />
<span class="wikidpad todo">todo: write a blog post about open science</span><br class="wikidpad" />
<span class="wikidpad todo">todo: write-up and publish my research agenda</span><br class="wikidpad" />
<span class="wikidpad todo">todo: Alien Species Profile for BDJ</span><br class="wikidpad" />
<span class="wikidpad todo">todo: research hypothes.is for my open lab notebook</span><br class="wikidpad" />
<br class="wikidpad" />
<a name=".h300" class="wikidpad"></a><h3 class="wikidpad heading-level3">Journal</h3>
<b class="wikidpad">2015-10-28</b><br class="wikidpad" />
This is my open lab notebook. Created a github pages website<br class="wikidpad" />
for my Phd thesis. On this website I will be hosting my<br class="wikidpad" />
open lab notebook (this) and <span class="wikidpad url-link"><a href="http://pdatascience.github.io/BiodivWiki/BiodiversityInformaticsLandscape.html" class="wikidpad">a small biodiversity-related wiki</a></span><br class="wikidpad" />
that I have been preparing on the side for my own references.<br class="wikidpad" />
<br class="wikidpad" />
Added a bunch of links from my Google drive. Since I will be posting<br class="wikidpad" />
a lot of links in this journal (in the text), wondering if there<br class="wikidpad" />
is a way to extract all links and put them in the end of the journal.<br class="wikidpad" />
Also wondering if I can use hypothes.is on this website to let people<br class="wikidpad" />
comment on it??<br class="wikidpad" />
<br class="wikidpad" />
<a name=".h941" class="wikidpad"></a><h3 class="wikidpad heading-level3">Links</h3>
<b class="wikidpad">Favorites</b><br class="wikidpad" />
DataOne API <span class="wikidpad url-link"><a href="https://releases.dataone.org/online/api-documentation-v1.2.0/apis/index.html" class="wikidpad">https://releases.dataone.org/online/api-documentation-v1.2.0/apis/index.html</a></span><br class="wikidpad" />
Programmable Web <span class="wikidpad url-link"><a href="http://www.programmableweb.com/" class="wikidpad">http://www.programmableweb.com/</a></span><br class="wikidpad" />
LinkedData.org <span class="wikidpad url-link"><a href="http://linkeddata.org/" class="wikidpad">http://linkeddata.org/</a></span><br class="wikidpad" />
NanoPub.org <span class="wikidpad url-link"><a href="http://nanopub.org/wordpress/" class="wikidpad">http://nanopub.org/wordpress/</a></span><br class="wikidpad" />
Global Biodiversity Information Facility <span class="wikidpad url-link"><a href="http://www.gbif.org/" class="wikidpad">http://www.gbif.org/</a></span><br class="wikidpad" />
<br class="wikidpad" />
<b class="wikidpad">Data Science and R</b><br class="wikidpad" />
<span class="wikidpad url-link"><a href="http://www.analyticsvidhya.com/" class="wikidpad">http://www.analyticsvidhya.com/</a></span><br class="wikidpad" />
Hacks to perform faster Text Mining in R<br class="wikidpad" />
<span class="wikidpad url-link"><a href="http://www.analyticsvidhya.com/blog/2015/09/learn-top-4-hacks-perform-text-mining-faster/?utm_source=feedburner&utm_medium=email&utm_campaign=Feed%3A+AnalyticsVidhya+%28Analytics+Vidhya%29" class="wikidpad">http://www.analyticsvidhya.com/blog/2015/09/learn-top-4-hacks-perform-text-mining-faster/?utm_source=feedburner&utm_medium=email&utm_campaign=Feed%3A+AnalyticsVidhya+%28Analytics+Vidhya%29</a></span><br class="wikidpad" />
<br class="wikidpad" />
<b class="wikidpad">Strategic planning (i.e. “Mission and Vision”)</b><br class="wikidpad" />
<br class="wikidpad" />
<span class="wikidpad url-link"><a href="https://www.psychologytoday.com/blog/smartwork/201004/vision-and-mission-whats-the-difference-and-why-does-it-matter" class="wikidpad">https://www.psychologytoday.com/blog/smartwork/201004/vision-and-mission-whats-the-difference-and-why-does-it-matter</a></span><br class="wikidpad" />
<span class="wikidpad url-link"><a href="http://www.richardbagshaw.co.uk/motivation/" class="wikidpad">http://www.richardbagshaw.co.uk/motivation/</a></span><br class="wikidpad" />
<br class="wikidpad" />
<b class="wikidpad">Some Links</b><br class="wikidpad" />
<br class="wikidpad" />
<span class="wikidpad url-link"><a href="https://zenodo.org/dev" class="wikidpad">https://zenodo.org/dev</a></span><br class="wikidpad" />
<span class="wikidpad url-link"><a href="http://www.refindit.org/" class="wikidpad">http://www.refindit.org/</a></span><br class="wikidpad" />
<span class="wikidpad url-link"><a href="https://www.overleaf.com/blog/87#.VX6usfmqpBd" class="wikidpad">https://www.overleaf.com/blog/87#.VX6usfmqpBd</a></span><br class="wikidpad" />
<span class="wikidpad url-link"><a href="http://www.cetaf.org/" class="wikidpad">http://www.cetaf.org/</a></span><br class="wikidpad" />
<span class="wikidpad url-link"><a href="http://geo.pbe.eionet.europa.eu/" class="wikidpad">http://geo.pbe.eionet.europa.eu/</a></span><br class="wikidpad" />
<span class="wikidpad url-link"><a href="http://www.pro-ibiosphere.eu/" class="wikidpad">http://www.pro-ibiosphere.eu/</a></span><br class="wikidpad" />
<span class="wikidpad url-link"><a href="https://rpubs.com/" class="wikidpad">https://rpubs.com/</a></span><br class="wikidpad" />
dataone R toolkit <span class="wikidpad url-link"><a href="https://releases.dataone.org/online/dataone_r/" class="wikidpad">https://releases.dataone.org/online/dataone_r/</a></span><br class="wikidpad" />
web clients for R <span class="wikidpad url-link"><a href="http://cran.r-project.org/web/packages/curl/index.html" class="wikidpad">http://cran.r-project.org/web/packages/curl/index.html</a></span><br class="wikidpad" />
<br class="wikidpad" />
<b class="wikidpad">API/JSON/Middleware</b><br class="wikidpad" />
<span class="wikidpad url-link"><a href="http://www.programmableweb.com/news/emergence-api-middleware-exclusive-interview-webshell.io/2013/10/02" class="wikidpad">http://www.programmableweb.com/news/emergence-api-middleware-exclusive-interview-webshell.io/2013/10/02</a></span><br class="wikidpad" />
<span class="wikidpad url-link"><a href="http://stackoverflow.com/questions/4035742/parsing-json-object-in-php-using-json-decode" class="wikidpad">http://stackoverflow.com/questions/4035742/parsing-json-object-in-php-using-json-decode</a></span><br class="wikidpad" />
<span class="wikidpad url-link"><a href="http://coreymaynard.com/blog/creating-a-restful-api-with-php/" class="wikidpad">http://coreymaynard.com/blog/creating-a-restful-api-with-php/</a></span><br class="wikidpad" />
<span class="wikidpad url-link"><a href="http://www.richardbagshaw.co.uk/laravel-5-middleware/" class="wikidpad">http://www.richardbagshaw.co.uk/laravel-5-middleware/</a></span><br class="wikidpad" />
very good stuff from spotify <span class="wikidpad url-link"><a href="https://developer.spotify.com/web-api/endpoint-reference/" class="wikidpad">https://developer.spotify.com/web-api/endpoint-reference/</a></span><br class="wikidpad" />
<br class="wikidpad" />
<b class="wikidpad">node js</b><br class="wikidpad" />
<span class="wikidpad url-link"><a href="http://www.infoworld.com/article/2866712/php/php-vs-node-js-an-epic-battle-for-developer-mind-share.html" class="wikidpad">http://www.infoworld.com/article/2866712/php/php-vs-node-js-an-epic-battle-for-developer-mind-share.html</a></span><br class="wikidpad" />
<span class="wikidpad url-link"><a href="http://www.intridea.com/blog/2010/4/29/rest-isnt-what-you-think-it-is" class="wikidpad">http://www.intridea.com/blog/2010/4/29/rest-isnt-what-you-think-it-is</a></span><br class="wikidpad" />
<span class="wikidpad url-link"><a href="http://adrianmejia.com/blog/2014/10/01/creating-a-restful-api-tutorial-with-nodejs-and-mongodb/#nodejs" class="wikidpad">http://adrianmejia.com/blog/2014/10/01/creating-a-restful-api-tutorial-with-nodejs-and-mongodb/#nodejs</a></span><br class="wikidpad" />
<span class="wikidpad url-link"><a href="http://www.programmableweb.com/" class="wikidpad">http://www.programmableweb.com/</a></span><br class="wikidpad" />
rpc vs api <span class="wikidpad url-link"><a href="http://restful-api-design.readthedocs.org/en/latest/methods.html" class="wikidpad">http://restful-api-design.readthedocs.org/en/latest/methods.html</a></span><br class="wikidpad" />
<span class="wikidpad url-link"><a href="http://etherealbits.com/2012/12/debunking-the-myths-of-rpc-rest/" class="wikidpad">http://etherealbits.com/2012/12/debunking-the-myths-of-rpc-rest/</a></span><br class="wikidpad" />
<br class="wikidpad" />
<b class="wikidpad">Linked Data</b><br class="wikidpad" />
an interesting doctoral thesis on music data <span class="wikidpad url-link"><a href="http://raimond.me.uk/phd/thesis.pdf" class="wikidpad">http://raimond.me.uk/phd/thesis.pdf</a></span><br class="wikidpad" />
tim berners lee <span class="wikidpad url-link"><a href="http://www.w3.org/DesignIssues/LinkedData.html" class="wikidpad">http://www.w3.org/DesignIssues/LinkedData.html</a></span><br class="wikidpad" />
the ultimate resource about linked data <span class="wikidpad url-link"><a href="http://linkeddata.org/guides-and-tutorials" class="wikidpad">http://linkeddata.org/guides-and-tutorials</a></span><br class="wikidpad" />
biosharing <span class="wikidpad url-link"><a href="https://www.biosharing.org/pages/about/" class="wikidpad">https://www.biosharing.org/pages/about/</a></span><br class="wikidpad" />
Linking is a public good<br class="wikidpad" />
<span class="wikidpad url-link"><a href="http://www.cs.ubc.ca/~murphyk/Papers/kv-kdd14.pdf" class="wikidpad">http://www.cs.ubc.ca/~murphyk/Papers/kv-kdd14.pdf</a></span><br class="wikidpad" />
<span class="wikidpad url-link"><a href="http://schema.org/docs/gs.html" class="wikidpad">http://schema.org/docs/gs.html</a></span><br class="wikidpad" />
<br class="wikidpad" />
<b class="wikidpad">Big Data</b><br class="wikidpad" />
a bunch of useful links on big data<br class="wikidpad" />
<span class="wikidpad url-link"><a href="http://www.analyticsvidhya.com/blog/2015/07/big-data-analytics-youtube-ted-resources/?utm_source=feedburner&utm_medium=email&utm_campaign=Feed%3A+AnalyticsVidhya+%28Analytics+Vidhya%29" class="wikidpad">http://www.analyticsvidhya.com/blog/2015/07/big-data-analytics-youtube-ted-resources/?utm_source=feedburner&utm_medium=email&utm_campaign=Feed%3A+AnalyticsVidhya+%28Analytics+Vidhya%29</a></span><br class="wikidpad" />
<br class="wikidpad" />
<b class="wikidpad">metadata</b><br class="wikidpad" />
<span class="wikidpad url-link"><a href="http://www.tdwg.org/" class="wikidpad">http://www.tdwg.org/</a></span><br class="wikidpad" />
<span class="wikidpad url-link"><a href="http://dublincore.org/" class="wikidpad">http://dublincore.org/</a></span><br class="wikidpad" />
<br class="wikidpad" />
<b class="wikidpad">XML</b><br class="wikidpad" />
<span class="wikidpad url-link"><a href="http://www.w3.org/XML/" class="wikidpad">http://www.w3.org/XML/</a></span><br class="wikidpad" />
<span class="wikidpad url-link"><a href="http://www.w3schools.com/xml/xml_whatis.asp" class="wikidpad">http://www.w3schools.com/xml/xml_whatis.asp</a></span><br class="wikidpad" />
comparison of rdf na xml <span class="wikidpad url-link"><a href="http://www.isi.edu/expect/web/semanticweb/comparison.html" class="wikidpad">http://www.isi.edu/expect/web/semanticweb/comparison.html</a></span><br class="wikidpad" />
<br class="wikidpad" />
<b class="wikidpad">RDF</b><br class="wikidpad" />
<span class="wikidpad url-link"><a href="http://www.w3.org/DesignIssues/RDF-XML" class="wikidpad">http://www.w3.org/DesignIssues/RDF-XML</a></span><br class="wikidpad" />
<span class="wikidpad url-link"><a href="http://www.isi.edu/expect/web/semanticweb/comparison.html" class="wikidpad">http://www.isi.edu/expect/web/semanticweb/comparison.html</a></span><br class="wikidpad" />
<br class="wikidpad" />
<b class="wikidpad">database</b><br class="wikidpad" />
<span class="wikidpad url-link"><a href="https://www.codeschool.com/courses/the-sequel-to-sql" class="wikidpad">https://www.codeschool.com/courses/the-sequel-to-sql</a></span><br class="wikidpad" />
<br class="wikidpad" />
<b class="wikidpad">php</b><br class="wikidpad" />
parsing JSON objects <span class="wikidpad url-link"><a href="http://stackoverflow.com/questions/4035742/parsing-json-object-in-php-using-json-decode" class="wikidpad">http://stackoverflow.com/questions/4035742/parsing-json-object-in-php-using-json-decode</a></span><br class="wikidpad" />
creating a RESTFul API <span class="wikidpad url-link"><a href="http://coreymaynard.com/blog/creating-a-restful-api-with-php/" class="wikidpad">http://coreymaynard.com/blog/creating-a-restful-api-with-php/</a></span><br class="wikidpad" />
rest isn’t what you think it is <span class="wikidpad url-link"><a href="http://www.intridea.com/blog/2010/4/29/rest-isnt-what-you-think-it-is" class="wikidpad">http://www.intridea.com/blog/2010/4/29/rest-isnt-what-you-think-it-is</a></span><br class="wikidpad" />
php vs node js <span class="wikidpad url-link"><a href="http://www.infoworld.com/article/2866712/php/php-vs-node-js-an-epic-battle-for-developer-mind-share.html" class="wikidpad">http://www.infoworld.com/article/2866712/php/php-vs-node-js-an-epic-battle-for-developer-mind-share.html</a></span><br class="wikidpad" />
<br class="wikidpad" />
<b class="wikidpad">intiatives, consortium</b><br class="wikidpad" />
EUDAT: the collaborative Pan-European infrastructure <br class="wikidpad" />
providing research data services, training and consultancy for<br class="wikidpad" />
<span class="wikidpad url-link"><a href="http://eudat.eu/" class="wikidpad">http://eudat.eu/</a></span><br class="wikidpad" />
<br class="wikidpad" />
<b class="wikidpad">Pensoft IPT</b><br class="wikidpad" />
<span class="wikidpad url-link"><a href="http://ipt.pensoft.net/manage/metadata-taxcoverage.do?r=testtag123" class="wikidpad">http://ipt.pensoft.net/manage/metadata-taxcoverage.do?r=testtag123</a></span><br class="wikidpad" />
<span class="wikidpad url-link"><a href="http://pwt.pensoft.net/document_auto_unlocked.php?document_id=4272" class="wikidpad">http://pwt.pensoft.net/document_auto_unlocked.php?document_id=4272</a></span><br class="wikidpad" />
<br class="wikidpad" />
<b class="wikidpad">Biodiversity Informatics Projects</b><br class="wikidpad" />
<span class="wikidpad url-link"><a href="https://sites.google.com/site/biosemanticsproject/" class="wikidpad">https://sites.google.com/site/biosemanticsproject/</a></span><br class="wikidpad" />
<span class="wikidpad url-link"><a href="http://etc.cs.umb.edu/etcsite/" class="wikidpad">http://etc.cs.umb.edu/etcsite/</a></span><br class="wikidpad" />
<br class="wikidpad" />
<b class="wikidpad">R</b><br class="wikidpad" />
<span class="wikidpad url-link"><a href="http://swirlstats.com/" class="wikidpad">http://swirlstats.com/</a></span><br class="wikidpad" />
<span class="wikidpad url-link"><a href="https://www.coursera.org/course/statistics" class="wikidpad">https://www.coursera.org/course/statistics</a></span><br class="wikidpad" />
cloud computing in R<br class="wikidpad" />
<span class="wikidpad url-link"><a href="https://www.linkedin.com/grp/post/77616-6024044391767826436" class="wikidpad">https://www.linkedin.com/grp/post/77616-6024044391767826436</a></span><br class="wikidpad" />
<br class="wikidpad" />
<br class="wikidpad" />
<b class="wikidpad">BeXiS Conference</b><br class="wikidpad" />
There are also some photographs under 'Impressions' and I posted a few thoughts on this event in a blog post:<br class="wikidpad" />
<span class="wikidpad url-link"><a href="http://fusion.cs.uni-jena.de/fusion/blog/2015/07/27/recapping-the-1st-bexis-user-and-developer-conference-0910-july-2015/" class="wikidpad">http://fusion.cs.uni-jena.de/fusion/blog/2015/07/27/recapping-the-1st-bexis-user-and-developer-conference-0910-july-2015/</a></span><br class="wikidpad" />
bexis slides<br class="wikidpad" />
<span class="wikidpad url-link"><a href="http://fusion.cs.uni-jena.de/bexis2userdevconf2015/program/" class="wikidpad">http://fusion.cs.uni-jena.de/bexis2userdevconf2015/program/</a></span><br class="wikidpad" />
<br class="wikidpad" />
<b class="wikidpad">Biodiversity Portals</b><br class="wikidpad" />
VertNet<br class="wikidpad" />
<span class="wikidpad url-link"><a href="http://www.vertnet.org/index.html" class="wikidpad">http://www.vertnet.org/index.html</a></span><br class="wikidpad" />
<br class="wikidpad" />
<b class="wikidpad">Emoji</b><br class="wikidpad" />
utf emoji codes<br class="wikidpad" />
<span class="wikidpad url-link"><a href="http://apps.timwhitlock.info/emoji/tables/unicode" class="wikidpad">http://apps.timwhitlock.info/emoji/tables/unicode</a></span><br class="wikidpad" />
<br class="wikidpad" />
<b class="wikidpad">Design Patterns</b><br class="wikidpad" />
MVC presentation<br class="wikidpad" />
<span class="wikidpad url-link"><a href="https://ist.berkeley.edu/as-ag/pub/pdf/mvc-seminar.pdf" class="wikidpad">https://ist.berkeley.edu/as-ag/pub/pdf/mvc-seminar.pdf</a></span><br class="wikidpad" />
<br class="wikidpad" />
<b class="wikidpad">Data Visualization</b><br class="wikidpad" />
Data visualization in R<br class="wikidpad" />
<span class="wikidpad url-link"><a href="http://www.analyticsvidhya.com/blog/2015/08/cheat-sheet-data-visualization-r/?utm_source=feedburner&utm_medium=email&utm_campaign=Feed%3A+AnalyticsVidhya+%28Analytics+Vidhya%29" class="wikidpad">http://www.analyticsvidhya.com/blog/2015/08/cheat-sheet-data-visualization-r/?utm_source=feedburner&utm_medium=email&utm_campaign=Feed%3A+AnalyticsVidhya+%28Analytics+Vidhya%29</a></span><br class="wikidpad" />
<br class="wikidpad" />
<br class="wikidpad" />
<br class="wikidpad" />
<ul class="wikidpad bulletlist">
<li class="wikidpad" /><span class="wikidpad wiki-link"><a href="WikiSettings.html" class="wikidpad">WikiSettings</a></span></ul>
</body>
</html>