Day 0: Software and training setup

Our lab uses a various software and webservices for digital infrastructure and organization. Before beginning work in the lab, you must complete all required Environment, Health & Safety (EHS) trainings. New grad students and postdocs should also install or set up accounts for everything listed here; others should ask their mentor which are essential.

Check off each task as you complete it on the lab Onboarding Form (download the one for grad students/postdocs or undergrads/visiting students). The most recent forms are also located in this folder in the lab SharePoint.

Important

Most of the software and webservices require an MIT ID/email. You should prioritize getting this set up. However, if you are waiting on paperwork, you can download most of the software (even if you won’t be able to log in yet). After that, you may wish to read through the Day 1, Day 2, and linked pages on the protocols site.

EHS setup and trainings

Adding yourself to the lab’s training group will register you with the EHS system and add all necessary trainings to your profile.

1. Go to https://atlas.mit.edu and go to the learning center, through the tab on the left:

   

2. In the upper right, select “My Profile”, then “Update PI/Activities”.

3. Add Kate E. Galloway as your PI.

4. Select the following training types (5 total). If you are an undergrad, do not select the BL2+ training group.

5. After submitting, many required trainings will be added to your Learning Center.

• Complete the online trainings. This will likely take a few hours!

• Some trainings have a required “classroom” component, such as the Lab Specific Chemical Hygiene training, which will be completed with an in-lab walkthrough.

• To complete the Signature: Read Dept. Chemical Hygiene Plan training, please read the Chemical Hygiene Plan and then sign the attestation form, available at: https://web.mit.edu/cheme/resources/lab/ehs/ehs_cert.html

Note

One of the components of the bloodborne pathogen training is the opportunity to be vaccinated for Hepatitis B or to have an antibody titer test for free.

Most of us were vaccinated for HepB as children, but that vaccine was only ~90% effective, so you may want to get the free antibody titer test. You can get a free booster or get doses of a new, more modern HepB vaccine if you no longer have HepB antibodies.

6. (Grad students and postdocs only) Also add and complete the following:

• Autoclave Safety Training, required for access to the autoclave/ice room.

• Shipping Training (new as of June 2026), required for shipping any materials on behalf of MIT.

• If you are going to be helping with mouse work, in the “My Profile” tab under “Training Groups” click “Join Another Group” and add the 68N: Mouse training group. Complete the additional trainings. Note that some of these require in-person trainings in the mouse facilities, which can be completed over the next few months.

Software and webservices

Core webservices

• Create a Github account. You can use either a personal or MIT email.

  • Activate your student benefits by going to https://education.github.com/discount_requests/student_application. You will be asked to connect your MIT email and send in a picture of your student ID. (Because MIT does not remove emails for alums, they need to confirm active student status.)

• Create a Zotero account. Using a personal email is recommended for permanence reasons.

• Create an ORCID. Adding all of your active emails is recommended.

• Request an MIT Google Workspace account. This provides access to Google services like Drive, Docs, Calendar, etc. Note that it may take 24 hours to activate. Alternatively, you can use a personal Google Account for access to a lab calendar.

• (New grad students and postdocs only) Create a Quartzy account. Using your MIT email is recommended.

After creating these accounts, request access to the lab’s group on the relevant webservices. Most of these are managed by one or two lab members; see the onboarding form for who to contact. Message them with the following information: your Kerberos ID (MIT email), your Github username, your Zotero username, the email you’d like added to the lab Google Calendar, and the email associated with your Quartzy account.

Then, you must accept the Github invitation to the GallowayLabMIT organization and the Zotero invitation to the gallowaylab group, checking that it appears in your group list.

Shared storage

We use two file storage services in the lab: OneDrive / SharePoint for “small” files like documents, plasmids, primers, posters, and so on, and Smithsonian / Nextcloud for data files (microscopy images, flow data, NGS data). We used to use OneDrive for everything, but OneDrive has a 5-TB storage limit, which we reached after seven years.

Luckily, you login to both Smithsonian and OneDrive through Touchstone, so you don’t need separate accounts.

(1) OneDrive / SharePoint

OneDrive is Microsoft’s file syncing service, and SharePoint is the version for teams (we use these terms interchangeably). The web interface of OneDrive is slightly clunky, and the official file syncing client is, honestly, not great. There are sync delays and sometimes things do not update. However, OneDrive has tight integration with Office products, allowing Google Drive-esque live, multi-person editing of Office documents saved within it. This is the largest reason why we still use OneDrive.

OneDrive uses “files-on-demand”/”online sync”, where all files in the shared storage appear to be accessible, but do not actually take up local disk space until you open them/unless you manually trigger a download, at which point the software invisibly downloads files in the background. There’s no cost to having the entire shared folder locally synced. Additionally, you can override this behavior and request that OneDrive download files before you access them (normally via a right-click menu)

After being given access:

1. If you are not on a recent version of Windows, download the OneDrive client. Recent versions of Windows come with this preinstalled.

2. Bookmark the web version here: https://mitprod.sharepoint.com/sites/GallowayLab/Shared%20Documents

3. On the web version, select the Sync button in the top tab:

   

4. This will trigger the OneDrive software you installed. It will ask you for a local folder to sync into (the default location is usually fine). After several minutes, it will show “OneDrive is up to date”, and all files should be accessible.

(2) Smithsonian

Smithsonian is the name of our data storage server that lives in the lab. We run this server ourselves, and it (currently) has a much larger capacity than OneDrive / Google Drive / MIT Dropbox: nearly 45 TB. Data stored on here is also backed up to an MIT-run backup system called Spectrum Protect / TSM. (If you’re curious how this works, see the tech documentation.) Our storage server is running software called Nextcloud Server. Unlike other cloud-syncing services, Nextcloud (the mostly open-source organization) does not run servers themselves, so our instance of Nextcloud is accessible at smithsonian.mit.edu.

Like OneDrive, there is both a web interface to quickly browse files, and a local sync client that you can download that lets you access the files. The Nextcloud sync client also does the same virtual-file / “files-on-demand” that OneDrive does. You can access the web interface at https://smithsonian.mit.edu. You will see a login page that looks like this:

The “Direct login” option is only used for special accounts that are not attached to a person, namely, the administrator account and the account that the lab computers use. Both of these account details are in the password database and are accessed as described in the tech documentation.

To login, use the MIT Touchstone option, which will redirect you through Touchstone and eventually land you on the files page:

Lab computers automatically save data into the data folder and are automatically shared with everyone. Other files and folders you create within your account are not shared with the lab by default (but are backed up and accessible with the administrator account).

To setup the local sync client, you need to download the Nextcloud client software and point it at Smithsonian.

1. Download the appropriate version of the Nextcloud Files app for your computer from the Nextcloud site.

2. Install the software.

3. Launch the software. It will ask you what server to connect to. Type in smithsonian.mit.edu

4. A web browser should open showing the Smithsonian login page. Login with Touchstone. You will reach a “grant access” page to allow sync access for this computer.

5. After granting access, return to the sync client. If it asks you to pick a location for the local sync folder, pick anything convenient. On macOS, it will appear in the default location: /Users/[your-user]/Library/CloudStorage/.

Coding and collaboration

• Slack is how we communicate! After downloading it, sign into https://gallowaylab.slack.com. In addition to the default channels, you may want to join #sequencing to get your sequencing orders delivered right to you via Slack, and join #memes for obvious reasons. Ask your mentor or point of contact to add you to any other relevant private channels.

• VS Code: Having a good plain-text editor (not Word) is important for coding, and is ultimately up to personal taste. We recommend Visual Studio Code (VS Code), downloadable here. However, if you have a different favorite editor, you may use that. If you are used to language-specific IDEs like MATLAB, IDLE, or RStudio, VS Code allows you to do editing, debugging, previewing, source control, etc in a mostly language-agnostic manner; once you customize it to your preferences, you can use it for all of your coding.

  After installing, you should click the extensions button:

  and search and install the following extensions (type in the name, click the install button).

  Recommended VS Code extensions

  Name	Image	Description
  Code Spell Checker		Inline spell checker that is intelligent enough to not flag specific language-specific words, but still can spell check comments and variable names.
  Esbonio		Support for editing Sphinx projects, e.g., this protocols site. The live preview function is super helpful!
  Jupyter		Inline Jupyter notebook support. No more need to launch Jupyter in a web browser, just do it inside VS Code!
  Pylance		Faster ‘language server’ for Python, which means the IntelliSense is faster and more accurate.
  Python		Enables Python debugging, running, and IntelliSense (in-line help while typing).
  R (optional)		Base language support for R.
  R LSP Client (optional)		The VS Code side of the R language server. Before installing this, run install.packages("languageserver") inside an R prompt.
  reStructuredText		Enables reStructuredText support, the language used to write this documentation, among others.
  reStructuredText Syntax highlighting		Enables syntax highlighting for reStructuredText.
  Snakemake Language		Snakemake syntax highlighting for editing computational pipelines.

• Git: For any code/code-like files (LaTeX, other plain-text files), Git is the standard way to share and collaborate with others and to track version history.

  You must install the base command-line tools from here. Select your operating system and not the “Download source code” button. For macOS, the easiest way is probably the “Xcode Command Line Tools” option.

  Tip

  When installing Git, you may want to change Git’s default editor to something other than Vim, such as VS Code.

  When asked about adjusting the PATH environment, choose the Git from the command line and also from 3rd-party software option; this makes sure all the other software also has Git access. All other defaults are fine, but can be changed if you want.

  After installation, you should set your global identity on that computer, i.e., the name and email that gets stored alongside the work you do. To do so, open a terminal (Terminal on macOS, Powershell on Windows) and type the following lines (without the beginning $, which identifies here that we are typing this into a terminal), substituting your name and email (giving an email you associated with your Github account). If you’re not familiar with the terminal, check out our intro here.

  $ git config --global user.name "Full Name"
  $ git config --global user.email email_address@example.com
  

  For a comprehensive introduction to Git, check out our intro here or this tutorial from Git.

• (Optional) Github Desktop: This program is a good basic GUI Git tool, in case the command line interface or built-in editor interfaces aren’t for you. Download it here.

• Python: Python is an excellent “Jack of all trades” language; we use it extensively. If you are on macOS, you may have Python3 pre-installed; you can check by typing python3 at a terminal. If you do not have Python preinstalled, you should download it here. Click the latest version download from the top, then scroll down and select the 64-bit installer for your OS.

  When installing, select Add Python to PATH; this ensures that when you type python at a terminal, you get this version you just installed. Other software can also access this “default” installation. After installing, restart VS Code.

  What is PATH?

  PATH is a “environment variable”, i.e., something that any program running in the “environment” of your computer can access. It is a list of folders where software can be found. In a command line, when you type a program name (like ls, or python, or git) without specifying where the program is, your computer iterates through every folder in PATH to see if it can find the program there.

  Bonus fact: virtual environments work by temporarily messing with PATH, redirecting calls to programs like Python to the virtual environment install.

  On snakes and Anaconda

  If you have Anaconda installed and don’t have an explicit reason to need it (e.g., conda-only packages), it is recommended to uninstall Anaconda and install Python directly this way.

  With modern Python, the benefits that Anaconda initially brought to the field (virtual environments and pre-compiled packages) are now integrated into the normal Python ecosystem, making Anaconda unnecessary. We also don’t want multiple Python versions competing.

  To make sure the install worked, open a new terminal and type python (or python3 on macOS), checking that the output looks similar to the following. Then exit the Python prompt by typing exit().

  $ python
  Python 3.9.1 (tags/v3.9.1) [MSC v.1916 64 bit (AMD64)] on win32
  Type "help", "copyright", "credits" or "license" for more information.
  

  Fixing Python “command not found” (Windows & macOS)

  If you see errors like

  • 'python' is not recognized as an internal or external command

  • command not found: python

  then you likely forgot do the above step (clicking Add Python to PATH), or you didn’t restart VS Code. The easiest way to fix this is to simply uninstall Python and reinstall it, while clicking the box. If you don’t want to do that for some reason, you can manually add Python to PATH.

  Windows

  You need to find where Python is installed. This will vary! The easiest way to do this is just search for python.exe to locate where that folder is. This might look something like

  C:\Users\<USERNAME>\AppData\Local\Python\python-3.14\python.exe

  Then:

  1. Press the Windows key on your keyboard to bring up the search.

  2. Search for Edit environment variables

  3. In the box that shows up, click Edit the system environment variables.

  4. Click Environment Variables.

  5. In the User variables for <USERNAME> box, find the Path variable and click Edit.

  6. In the list of directories that shows up, click New and add the folder containing Python identified earlier.

  7. Click OK and restart any open terminals and VS Code to pick up the change. (If you’re unsure, log out and log back in to your computer.)

  macOS / Linux

  On macOS and Linux, you handle the path by editing your shell configuration file, normally either at ~/.zshrc for zsh or ~/.bashrc for Bash.

  In these lines, you should add an export call to add the Python location to the end of path, like:

  export PATH="$PATH:/path/to/python/that/you/found

• (Optional) R: Many bioinformatics tools are written in R, but there are also many good Python versions. You can install this now, or wait to see if you need it later. From here, download the main package (macOS) or both the base entry and the Rtools entry (Windows).

• (Optional) RStudio: If you don’t feel like using VS Code for your R work, the excellent, well-polished standard IDE is RStudio Desktop, downloadable here.

Experimental software

• SnapGene: We use SnapGene for molecular cloning and plasmid design. Download it through MIT IST here, and access the registration code here (MIT login required for both links).

• FlowJo: We have a single license on lab computers for analyzing flow cytometry data; we can show you how it works in-lab.

• (Optional) FIJI: For simple image analysis, Fiji (ImageJ) gives a nice GUI interface. Download it from https://fiji.sc

• (Optional) CellProfiler: CellProfiler is an excellent tool for doing image cytometry (analyzing cell-by-cell in image data). In contrast to the GUI-only tools built into the Keyence software, CellProfiler enables repeatable, pipelinable analyses. Download it from https://cellprofiler.org/

Other

• Zotero: Zotero is an excellent free, open-source citation manager. After downloading Zotero from https://www.zotero.org/, it should prompt you to install the Zotero Connector, a browser plugin that lets you download paper citations with one click. If it doesn’t prompt you, download the connector here. We also have a shared Zotero group, which you should have requested access to above, to accumulate citations when writing manuscripts.

  Several helpful plugins can be downloaded; the recommended ones are:

  Recommended Zotero plugins

  Name	Description
  ZotFile	Enables useful file operations, such as extracting annotations from a marked-up PDF, transferring new papers to a tablet for annotation, and auto-file renaming.
  Zutilo	Enables helpful tagging operations, such as the ability to copy/paste tags or easily add paper relationships.
  Better Bibtex	If you plan to use LaTeX, install this plugin before exporting to BibTeX. This addon makes nice-looking, stable citation keys that do not change on export.

  Downloading Zotero plugins through Firefox

  Since Zotero is built on modified Firefox, Zotero plugins appear similar to Firefox plugins. If downloading these plugins through Firefox, you will need to explicitly right click -> “download target”; left-clicking on download links will attempt to install the Zotero plugin as a Firefox plugin, which will fail.

• Better Quartzy:

  TODO

  Unfortunately, the Quartzy interface updated, so our userscript to customize the appearance is broken. :(

  While Quartzy is great for inventory purposes and the interface for the plasmid database isn’t too bad, the web interface leaves a lot to be desired. By default, you can’t really read the plasmid names even after you move the “CAS #”” field to the second position:

  

  To fix this, there is a Quartzy enhancer to make the plasmid field larger and to directly list the antibiotic resistance (Amp/Kan/Chlor) below the plasmid.

  

  This feature is implemented using something called userscripts; these are small Javascript scripts that get injected into webpages; effectively they are mini browser extensions.

  To set this up, install a userscript manager like Tampermonkey.

  Then, click on this link to add the userscript: https://gist.github.com/meson800/f28e64d532da9b0fe2a1d22480ea5cda/raw/quartzy_enhancer.user.js

  Or, in the Tampermonkey Utilities tab, you can use the install from URL option:

  

• Adobe Creative Cloud: MIT has a site license for students and staff (but unfortunately, not for affiliates). After installing the Creative Cloud application, select “Work/School account” and login with your MIT credentials. You may have to wait 24 hours for activation after your first login. You should install Acrobat (for viewing PDFs) and Illustrator (for drawing graphics).

  Note

  As a free and open-source alternative to Adobe Creative Cloud, you can also check out Inkscape (download here). Inkscape and Illustrator have many similar but not completely overlapping features. Inkscape’s PDF importer (Cairo) may be superior for importing vector images from manuscript PDFs. Inkscape may be useful to know if you don’t want to pay for Creative Cloud later; however, we use Adobe software for creating graphics and figures in lab.

• Color palettes: Having nice color-blind friendly, distinct colors is helpful when you begin creating graphics. Palettes help unify figures and convey consistent information via color.

  You can download pre-created palettes for both Illustrator and Inkscape for the well-known Category20/20b color set, which is color-blind friendly (and becoming the default in more and more software packages):

  

  To use these palette files, see the Illustrator documentation (“Create and open swatch libraries”) or the Inkscape documentation.

• Fonts: Helvetica Neue is a good sans-serif font that is based on everyone’s favorite font, Helvetica. While not required, many people in lab use this font, so their files (e.g., PowerPoint, Illustrator) won’t render well if you don’t have it installed. First, download it here (macOS, Linux) or here (Windows). Then, unzip the folder, select all the .tff files, and double click to open, which should prompt installation. Alternatively, right click and select “Install font”.

  For a good monospaced/code/terminal font, Fira Code is excellent (download here). Besides looking nice, Fira Code has something called font ligatures. These are originally defined for special letter combinations, like æ for adjacent ae. In Fira Code, common programming combinations are given special ligature symbols that appear as you type normally. You often have to enable ligatures in the editor you are using.