Citation and bibliographic references are integral part of scientific writing. To improve productivity and pace of writing, consider installing third-party citation management software such as Zotero, Mendeley, EndNote, etc. Among these, Zotero and Mendeley are available for free but, EndNote is paid.

See comparisons between Zotero, Mendeley, and EndNote, and decide which one you want to use.

• https://libguides.northwestern.edu/howtochoose
• https://guides.lib.uchicago.edu/c.php?g=297307&p=1984557
• https://libguides.wustl.edu/choose

In addition to having a freemium version, Zotero and Mendeley can be synced to Overleaf, and Zotero can be synced to Obsidian, a markdown-based text editor and knowledge management program (see below). If you have used Mendeley and EndNote, please add your experience here.

Zotero can be used locally and via the web. The default installation of Zotero comes with MS Word Plugin. Install https://retorque.re/zotero-better-bibtex/ Better BibTeX plugin to export .bib files for LaTeX. You can create libraries (folders/ subfolders) for different projects and drag and drop PDFs to Zotero to generate citations. There is no storage restriction for local use. You can also use a Zotero web account and add citations using your browser extension. One of the shortcomings of web account-based sync (especially to multiple devices) is the 300 MB of storage space for the free account. To avoid running to storage limit, you can drag and drop PDF with Cmd+Option keyboard shortcut on macOS or Ctrl+Shift on Windows or use Attach Link to File option from the app.

Mendeley operates almost similarly to Zotero, but the web-based storage space is 2GB for a free account.

EndNote is available for JHU affiliates. Check here: https://guides.library.jhu.edu/citing/endnote.

Hopkins provides Microsoft Office packages and OneDrive with 5 TB space for each student and postdoc. You can install Microsoft Office on up to 5 devices. Take advantage of the OneDrive storage to store your data. Additionally, Hopkins also provides access to premium Overleaf accounts for its affiliates. Overleaf is an online-based LaTeX editor and compiler (details are below).

We have a shared OneDrive for lab members; please contact Vicky for access.

If you are making your presentation on PowerPoint, here: A simple PowerPoint template for JHU.

• This is an example template. You are not required to use this. You can create your template but make sure you adhere to the university guidelines.
• This template uses the Johns Hopkins University logo and suggested color palette for the presentation.
• You can download the file and do File → Save as Template to make it appear as a template on the PowerPoint home page. Make sure to save the file with .potx extension instead of .pptx.
• To make changes to the template, go to View → Master Slide and then make changes. Once you're done making changes, save the file as a template using the .potx extension.

LaTeX is a document markup language for the TeX typesetting program. Most people use it because of its facility for typesetting mathematical equations, figures, and tables. Go to the Latex Project http://www.latex-project.org/ for more information.

A popular cloud-based alternative to the local LaTeX compiler and editor is Overleaf. The basic version of Overleaf is free, and Hopkins provides a premium version to its students and faculties. You can share the .tex file or project with multiple collaborators, and review and edit it online. Check it out here: https://www.overleaf.com/. Use your Hopkins email to activate the premium version.

To use LaTeX locally on your machine, you will need to download, the TeX programs, macros, fonts as well as and Latex editor. There are several packages available for Mac and Windows. For Mac, I recommend MacTex http://tug.org/mactex/ because it's easy to install and robust. For Windows, MikTeX is a commonly used package (http://miktex.org/). MikTeX on Windows works similarly to MacTex. For Linux, use TexLive; works the same as MacTex and MikTeX.

• You may find these regular LaTeX templates (article, report, beamer) useful for your work: https://github.com/NguyenLabJHU/LaTeX-Templates/
• An unofficial LaTeX template for Johns Hopkins thesis and dissertation on GitHub: https://github.com/NguyenLabJHU/JHU-Dissertation-Template.
• An unofficial LaTeX template for Mechanical Engineering PhD dissertation proposal on GitHub: https://github.com/NguyenLabJHU/JH-MechE-Dissertation-Proposal-Template.

You can clone or download these templates from GitHub and continue working on them locally on your computer if you have installed the LaTeX editor and compiler. Alternatively, you can find these templates on Overleaf and start working from there by using Open as Template.

For any JHU-related template, it is your responsibility to ensure the template is in conformation with university or department requirement and guidelines.

For a few lab members (Bibek and Tingting), the common workflow to use LaTeX equations on PowerPoint presentations is to use LaTeXiT locally. Using LaTeXiT-generated equations on PowerPoint slides requires the installation of BasicTeX, Ghostscript, and LaTeXiT. BasicTeX is a lightweight TeX distribution (only a few hundred megabytes) of MacTeX, Ghostscript is a rendering package of PostScript and PDF, and LaTeXiT is a very lightweight equation editor.

1. Download basictex and ghostscript from here: https://www.tug.org/mactex/morepackages.html.
2. Install in this order; first BasicTeX and then Ghostscript. Both of these come as .pkg files, so the installation procedure is straightforward and no customization is necessary.
3. Now download and install LaTeXiT from here: https://www.chachatelier.fr/latexit. The installation process is trivial.
4. Ordered LOpen LaTeXiT and then from the Menu bar on the top of the screen, go to Settings. Make sure your export format is “PDF Vector Output”. You can also export the equations in .png, .jpg, .tiff, .eps, and .svg format, but I found PDF to be the most compatible format which you can easily edit later by dragging and dropping to LaTeXiT.

You can now start typing equations and if you click on the LaTeXiT icon, it will produce the beautifully crafted LaTeX formula in the preview box on the top. You can drag it to the Desktop Window and it will be saved as a PDF file. You can also directly drag it to PowerPoint slides. It will embed there as an image. If you’d like to edit the equation later, you can drag that image to the preview window of LaTeXiT, it will generate the .tex code for you which you can edit and repeat the process of drag and embed. There is one thing that should be mentioned about this workflow: BasicTeX does not have all the packages you may need and manual installation of the packages might be needed. We will see soon how to do that.

If you’d like to see what LaTeX packages are installed in your distribution:

$ tlmgr list --only-installed

To install the additional packages, such as doublestroke and mathtools, use the following:

$ sudo tlmgr install doublestroke mathtools

To set a custom preamble in LaTeXiT, go to settings → Templates, then add the following code snippet and save it. Make this preamble template default for you for future use. This is just an example. You can add more packages (may have to install them) and macros as you need.

\documentclass[12pt]{article}

\usepackage[utf8]{inputenc}

\usepackage{amsfonts,amssymb,amsmath,amsthm,dsfont,mathtools,mathbbol,upgreek}
\usepackage[usenames]{color}
\usepackage{enumitem}
\usepackage[T1]{fontenc}

\newcommand{\dC}{$^{\circ}$C}
\DeclareMathOperator{\R}{\mathrm{R}}
\DeclareMathOperator{\T}{{\top}}
\newcommand{\vect}[1]{\mathbf{#1}}
\newcommand{\mat}[1]{\mathrm{#1}}
\DeclareMathOperator{\tr}{tr}
\DeclareMathOperator{\sym}{sym}
\DeclareMathOperator{\skw}{skw}
\DeclareMathOperator{\divg}{div}
\DeclareMathOperator{\grad}{grad}
\DeclareMathOperator{\curl}{curl}
\DeclareMathOperator{\sgn}{sign}

For Windows, you can also consider the PowerPoint plug-in IguanaTeX (https://www.jonathanleroux.org/software/iguanatex/). It's been a while since I installed it (that too on macOS). I would suggest following the instructions on the website and GitHub repository.

For macOS with Apple Silicon processors, IguanaTeX requires running PowerPoint using the Open with Rosetta option, and using the same equations outside of PowerPoint is not possible.

Markdown is a lightweight markup language that is also very readable compared to TeX, HTML, and others. Markdown has gained popularity in the last decade for taking notes, publishing simple web pages, making presentations, etc. You can use a dedicated Markdown editor such as Typora (yet another software) or even better you can use VS Code (see the Software and Computing wiki page for details).

• Getting started with Markdown page will give you an idea of what you can do with it.
• If you want to be very organized in taking notes for your research and class, you can consider Obsidian.

If you are already frustrated between writing the same thing in multiple markup languages, then look no further, Pandoc is here to save your day. Virtually, you can convert any form of document reasonably to another form using Pandoc.