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Academic research takes long and it's hard. You have to find, download, organize, read and cite relevant papers in your own paper. When you are dealing with hundreds of papers, it becomes a way too much daunting task. you have to use some tools to make it easier. I would like to share the tools and services I use or know that might help you.

Searching and Organizing Papers

My current best resource for finding papers is Google Scholar. I can see titles, abstracts and sometimes obtain PDF forms of the papers. Then I download them to a folder, and import to Mendeley by dragging and dropping the pdf files. Mendeley automatically extracts the title, abstract, authors, year, journal etc in many cases. If it fails to do so, you can fix it manually. You can put papers into folders, sub-folders, tag the files, write your own notes for each paper. It synchronizes your papers with its cloud (not Dropbox) so that you can read your papers anywhere, even on your iPad. A popular alternative is Zotero and a recent open source collaborative alternative is Scientilla where scientists collaborate for forming a bibliography base.

Writing your paper

When you want to write your own paper, you can use any editor. Using something like Word is hard when you deal with references and table of contents. If you have mathematical notations, you should go with LaTeX. You can use either TexMaker app or Atom editor with LaTeX plugin. LaTeX will get the references and table of contents working properly without requiring any manual operation other than citing. When citing, you will be using citation key e.g. \cite{Meinstein2009a}. To find the citation key of a paper, you can press CMD+K or Ctrl+K to copy the citation key in the Mendeley. Then you can paste it in your editor (I hope they implement a drag and drop interface for this in the future). You can then export your paper as a PDF file.

If you won't use mathematical notations, then using Markdown syntax would be the easiest and cleanest option. You can use Markdown syntax in a file with .md extension and then use Pandoc to compile it to PDF or HTML formats. Atom editor has a Markdown syntax highlighting package, a Markdown preview package you can install.

Another option is Scrivener app, which is not free but allows you to try it for 30 unique days for free. It provides organizing chapters, sections, subsections in a hierarchical manner over a tree so that you can move subsections from a branch to another and reorganize your paper easily. Most importantly, you only focus on the section you are working on and not distracted by other sections. In Scrivener, you can also write your paper in Markdown, use citation keys in brackets:

[#Meinstein2009a]

When you need using external citations like URLs which won't be added to Mendeley, you can use BibDesk to create citations manually. Scrivener has an Markdown to Latex conversion feature where it will create latex files with headers (document definition etc) and footers (end document) you specify. You will be specifying which bib files to use in the footer.

If you are using numeric references, you may want to sort them in increasing order. To do this, you can use my app Citation Sorter.

Collaboration

You may want to collaborate with your peers while writing your paper. If you are using LaTeX, you can use Overleaf or ShareLaTex which are online LaTeX editors with preview, collaboration and history features. They provide several templates of popular journals and conferences. Overleaf also allows you submit your paper directly to PeerJ journals. Authorea on the other hand, provides richer features like Markdown, Python notebook and d3.js visualization support.

If you don't use LaTeX, you can use Google Drive's text editor which allows collaboration. Then you may want to convert it into markdown and then PDF.

Presentations

You can use Markdown and pandoc also for presentations. Each section is a slide, and the content is the slide content. You can use bullet points as well. This method is much more easy to create slides than using your mouse. Pandoc will use Beamer to create PDF slides. You can specify custom beamer themes like Warsaw which is my favorite.

If you would like to produce interactive HTML presentations, you can use reveal.js which also uses Markdown and converts it to HTML slides.

If don't mind using your mouse, you can use slid.es web interface which uses reveal.js on the backend and produces html slides.

Coding Environment

If you have any computational need, I recommend Python programming language and PyCharm IDE. PyCharm has a free community edition and a paid version which provides more advanced features which you might not really need. There are some other IDEs like Anaconda Scientific Python IDE which provides many scientific libraries.

Another language I would be recommending is R Language. R is great at processing tables and matrix transformations, performing statistics and machine learning operations. RStudio will help you a lot with its Rmd file support where you can write tutorial-like R code and export all the explanations, codes and outputs to HTML or PDF, resulting reproducable reports.

Utilities

Your research is your everything so you have to take backups. Dropbox, Google Drive or SpiderOak are good services where you can both backup your files or use them as a synchronization service so that you can access your work both at the office and at home and even mobile! SpiderOak provides zero-knowledge policy where your data is encrypted before being transmitted to SpiderOak server. If you forget your password, your data is gone.

If you just want to take text or multimedia notes and access them anywhere, Evernote will be your friend. It works both on desktop and mobile.

Archiving your papers

Receiving response from journals take a lot of time. To prove that you have done the research at the first place, you may want to get a timestamp from an authority. Arxiv is one of these services where you can submit your work, get a timestamp and then submit your work to a journal so that nobody else can claim the ownership your work before yours is published. However the subjects are limited to few, mostly Physics, mathematics, computer science, statistics, biology, quantitative finance. You must be endorsed by somebody who has arxiv publication or be a co-author in an arxiv paper to be able to publish on arxiv. On the other hand, PeerJ PrePrints do not have such restriction but your work is analyzed for appropriateness before being accepted. You can publish case studies, opinion letters, etc which wouldn't be a journal paper or use it like arxiv to get a timestamp before submitting to a journal. You can even get feedback for your work before submitting it to a journal.


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