{"id":56,"date":"2008-07-05T14:07:05","date_gmt":"2008-07-05T14:07:05","guid":{"rendered":"http:\/\/www.mtheory.co.uk\/wordpress\/burly\/?p=56"},"modified":"2008-07-05T14:08:15","modified_gmt":"2008-07-05T14:08:15","slug":"thesis-tools","status":"publish","type":"post","link":"http:\/\/www.mtheory.co.uk\/wordpress\/burly\/archives\/56","title":{"rendered":"Thesis tools"},"content":{"rendered":"<p>Not that anyone cares of course, but I&#8217;ve now started to write up my PhD. I spent a long time agonising over whether to use Word or LaTex. In the end the lack of decent reference management tools for Word persuaded me that I should just learn LaTex and get on with it. \u00c2\u00a0Yes I know Endnote exists, I also know there&#8217;s citation available with in Word now and yes I&#8217;m also aware of Bookends and Zotero. I&#8217;ve not used Bookends in real anger nor Zotero and Word 2008&#8217;s reference management is rather limited and frustrating to use.\u00c2\u00a0<\/p>\n<p>So LaTex uses Bibtex for reference management and it&#8217;s fairly simple. Bibtex generates a flat text file with all you references\u00c2\u00a0formatted\u00c2\u00a0the way you want and then merges them into LaTex for you.. well it&#8217;s typeset LaTex, Bibtex, LaTex, LaTex. The nice thing about it is that unlike Endnote it&#8217;s simple and you don&#8217;t find the interface crashing or refusing to let you edit things. But still things aren&#8217;t idea. My workflow currently looks like this.<\/p>\n<ul>\n<li>OS is Mac OS X 10.5.3 with <a href=\"http:\/\/www.tug.org\/mactex\/\" target=\"_self\">MacTex 2007<\/a> installed<\/li>\n<li>I&#8217;m currently using <a href=\"http:\/\/www.uoregon.edu\/~koch\/texshop\/\" target=\"_self\">TexShop<\/a> for editing my LaTex files because it&#8217;s nice and simple. Output is pdftex.<\/li>\n<li>I&#8217;m managing all the journal papers I need with <a href=\"http:\/\/mekentosj.com\/papers\/\" target=\"_self\">Papers<\/a>, which is in essence iTunes for journal papers. I&#8217;m using it to export the references to Bibtex.<\/li>\n<li>However papers doesn&#8217;t fully support all the features of Bibtex so I&#8217;m also using <a href=\"http:\/\/bibdesk.sourceforge.net\/\" target=\"_self\">BibDesk<\/a>. It&#8217;s be nice if you could use just papers.<\/li>\n<li>I&#8217;ve also installed <a href=\"http:\/\/skim-app.sourceforge.net\/\" target=\"_self\">Skim<\/a> to enable commenting on PDFs similar to what you can do with <a href=\"http:\/\/www.zotero.org\/\" target=\"_self\">Zotero<\/a>.\u00c2\u00a0<\/li>\n<li>I&#8217;m using <a href=\"http:\/\/www.tweakersoft.com\/vectordesigner\/\" target=\"_self\">VectorDesigner<\/a> for my vector graphics, it&#8217;s not as powerful as <a href=\"http:\/\/www.adobe.com\/products\/illustrator\/\" target=\"_self\">Illustrator<\/a>, but it is easier and quicker to use not to mention cheaper. Plus I&#8217;m not sure I want to spend ages drawing really beautiful figures.<\/li>\n<li><a href=\"http:\/\/www.pixelmator.com\/\" target=\"_self\">Pixelmator<\/a> is sitting in the sidelines for the odd bit of raster work. Again it&#8217;s a cut down version of <a href=\"http:\/\/www.adobe.com\/products\/photoshop\/family\/\" target=\"_self\">Photoshop<\/a>. So far I&#8217;ve not needed it.<\/li>\n<li>Plotting is taking place in <a href=\"http:\/\/www.originlab.com\/\" target=\"_self\">Origin 8<\/a> which means I also need Windows installed. This is under <a href=\"http:\/\/www.virtualbox.org\/\" target=\"_self\">Virtual Box<\/a> which unlike <a href=\"http:\/\/www.vmware.com\/products\/fusion\/\" target=\"_self\">VMware<\/a> and\u00c2\u00a0<a href=\"http:\/\/www.parallels.com\/\" target=\"_self\">Parallels<\/a>\u00c2\u00a0is free. The interface isn&#8217;t as refined though. Origin definitely isn&#8217;t the ideal plotting program but a lot of my data is already in Origin and it&#8217;s very quick to use.<\/li>\n<li><a href=\"http:\/\/www.python.org\/download\/mac\/\" target=\"_self\">MacPython<\/a> with <a href=\"http:\/\/numpy.scipy.org\/\" target=\"_self\">numpy<\/a>, <a href=\"http:\/\/www.scipy.org\/\" target=\"_self\">scipy<\/a>, <a href=\"http:\/\/matplotlib.sourceforge.net\/\" target=\"_self\">matplotlib<\/a> and <a href=\"http:\/\/ipython.scipy.org\/moin\/\" target=\"_self\">ipython<\/a> is there for generating some plots and more importantly simulating various things. The output is often saved to text files and then plotted up in Origin. Partly because re-plotting all my data in matplotlib would be too time consuming.<\/li>\n<li>I also have <a href=\"http:\/\/www.arizona-software.ch\/graphclick\/\" target=\"_self\">GraphClick<\/a> there for lifting the odd bit of data from someone else&#8217;s paper.<\/li>\n<li>Finally my entire set of thesis files is under version control using <a href=\"http:\/\/www.selenic.com\/mercurial\/wiki\/\" target=\"_self\">Mercurial<\/a>. This allows me to commit regularly and revert if needed. It&#8217;s also pushed onto a web server so I can sync across my home machine and college machine.<\/li>\n<\/ul>\n<p>So that&#8217;s it at the minute. I should note that everything was also under <a href=\"http:\/\/www.apple.com\/macosx\/features\/timemachine.html\" target=\"_self\">Time Machine<\/a>, but due to a lack of spare hard drives currently isn&#8217;t. Though that will be resolved shortly. It&#8217;s quite a lot of software and that&#8217;s before you include the everyday tools such as the web browser, pdf viewer, mail client and of course Office as a lot of my older papers and conference presentations are in Word and Powerpoint.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Not that anyone cares of course, but I&#8217;ve now started to write up my PhD. I spent a long time agonising over whether to use Word or LaTex. In the end the lack of decent reference management tools for Word &hellip; <a href=\"http:\/\/www.mtheory.co.uk\/wordpress\/burly\/archives\/56\">Continue reading <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":2,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"ngg_post_thumbnail":0,"footnotes":""},"categories":[4,12],"tags":[16],"class_list":["post-56","post","type-post","status-publish","format-standard","hentry","category-apple","category-work","tag-phd-thesis"],"_links":{"self":[{"href":"http:\/\/www.mtheory.co.uk\/wordpress\/burly\/wp-json\/wp\/v2\/posts\/56","targetHints":{"allow":["GET"]}}],"collection":[{"href":"http:\/\/www.mtheory.co.uk\/wordpress\/burly\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.mtheory.co.uk\/wordpress\/burly\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.mtheory.co.uk\/wordpress\/burly\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"http:\/\/www.mtheory.co.uk\/wordpress\/burly\/wp-json\/wp\/v2\/comments?post=56"}],"version-history":[{"count":0,"href":"http:\/\/www.mtheory.co.uk\/wordpress\/burly\/wp-json\/wp\/v2\/posts\/56\/revisions"}],"wp:attachment":[{"href":"http:\/\/www.mtheory.co.uk\/wordpress\/burly\/wp-json\/wp\/v2\/media?parent=56"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.mtheory.co.uk\/wordpress\/burly\/wp-json\/wp\/v2\/categories?post=56"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.mtheory.co.uk\/wordpress\/burly\/wp-json\/wp\/v2\/tags?post=56"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}