MacManes Lab Onboarding Document

Mission Statement

The MacManes lab strives to be an internationally recognized leader in the field of ecophysiological and evolutionary genomics. To accomplish this goal, we push ourselves to be careful in our observations, broad in our questions, and vigorous in our pursuit of research funding. We are generous in the dissemination our products. Indeed, our vision for the future of science is collaborative more so than competitive. To this end, lab members should be prepared to develop the ability to:

1. Think criticaly, and quantitatively about biological phenomena.
2. Write code to analyze high-throughput sequence data.
3. Treat data analytics the same way you do a wet-lab or field work - as an experiment.

General Keys to Success

One key to success is to make other people say no to you (rather than you saying no to yourself). Don't not apply for some fellowship/job/position because you don't feel qualified. It's good to be realistic about your qualifications, but imposter syndrome (https://www.chronicle.com/article/Impostor-Syndrome-Is/238418) is real, and powerful.

Another important key to success is persistance. Seriously, you are going to be rejected far more frequently (jobs, papers, grants, etc) than not. Keep at it! Don't take it personally, and submit your paper somewhere else!

Positive attitude. Grad school is a ton of work, but this is all supposed to be fun and exciting. You are getting paid at this point to learn, discover, explore. That's wicked cool! Having a positive attitude, at least most of the time, is going to help you, and everyone around you. It's not always easy, and we're all human, but let's try..

Lab Expectations

We expect lab members to fully imerse themselves in the process of research and its dissemination. To accomplish this, we will conduct careful and reproducible experiments, write good code, and disseminate our results widely through approachable publications. When we submit papers, we expect that the analytical code behind those papers will be something that we can be proud of. To these ends, we will provide reviewers and the scientific community with all source code required to conduct analsyes in the paper that result from computational analyses.

About being a good lab citizen. You are expected to share freely, and without conditions, with your lab mates. This includes data, protocols, code, and other information. Unless you paid for the data yourself, it does not belong to you, it belongs to the lab. It’s my job as the PI to make sure you are properly credited via authorship, etc. I promise that you will get the credit you are due for the work you have done.

About email/slack One of the amazing things about academia is that you have a lot of freedom to set your own hours. Some of us have/had small children, and so normal business hours don't really work. I work when I can, and sometimes this is on the weekend, at night, early AM. Just because I do this, does not mean that I expect you to. If I send you an email at 0200 (see below tweet), I don't expect immediate action.

Your Role

Your role in the lab is to take primary responsibility for the success of your research project and career development. As a member of the lab, you are expected to participate fully in the team, which includes supporting others in their endeavours, and mentoring more junior members. In general lab members are expected to be present from 9:00AM to 3:00PM on weekdays to facilitate discussion within the group.

Matt’s Role

Matt’s goal is to facilitate your success as well as that of your project. Within your project, Matt will serve as a sounding board for ideas, will help you plan your project, and will help to devise experiments to test your hypotheses. For your success, Matt will help you to plan your training, to devise a career plan that takes you where you want to go, to manage your portfolio of project risk, and other elements of professional development.

Code of Conduct

All members of the lab, along with visitors, are expected to agree with the following code of conduct. We will enforce this code as needed. We expect cooperation from all members to help ensuring a safe environment for everybody.

The Specifics

The lab is dedicated to providing a harassment-free experience for everyone, regardless of gender, gender identity and expression, age, sexual orientation, disability, physical appearance, race, or religion (or lack thereof). Sexual images in public spaces, deliberate intimidation, stalking, following, harassing photography or recording, sustained disruption of talks or other events, inappropriate physical contact, and unwelcome sexual attention will not be tolerated.

Members asked to stop any harassing behavior are expected to comply immediately.

If you are being harassed, notice that someone else is being harassed, or have any other concerns, please contact Matt immediately. For official concerns, please see the University of New Hampshire ombuds office.

We expect members to follow these guidelines at any lab-related event.

See the original doc related to the code of conduct.

You will also be required to conduct University wide training on maintaining professional workplace envrionments. These will be emailed to your unh email account.

Parking

Postdocs will get a faculty/staff permit that will allow them to park in the Gregg Hall lot. You'll have to go the Parking office (https://unh.edu/transportation/parking).

For grad students, you also will get a permit (same office), but this will only allow you to park in A-lot (located right next to the parking permit office, across the street from the 'Field House'). You should ask another of the grad students for those details.

NOTE: You will need your "nine number" to get your permit (this should have been given to your in your 'welcome email', if you don't have one, contact UNH IT to get it). Get your permit BEFORE or AFTER the first week of classes, or get to the parking permit office right when they open.

Accounts

Information on how to get accounts on computers and in the services that the lab uses are below.

Email: UNH will assign you an email

Postdocs: [e-mail]
Grad Students: [e-mail]

This information and your 'nine number' (a long numeric identifier) should be in a 'welcome email; that you will recieve soon after you start. If you don't receive an email, don't fret! You can contact UNH IT (https://www.unh.edu/it/) and they'll set you up with a temporary password to get you started.

Cloud-based Services

1. The new member should learn what Github is as well as how to use it.
   • https://github.com/
2. The new member should create a HackMD account, which will allow access to this document.
   • https://hackmd.io/
3. The new member should be added to Slack.
   • https://slack.com/
   • There's android/apple apps for your phone and a stand-alone app for your laptop, or you can access it online.

Github Repositories

All code written for the lab should be committed to a repository with the macmanes-lab organization as the owner. This helps us to maintain continuity and provides a single location for our code. You can make your code private or public.

If you make your code public, we have certain expectations:

It will be under an open source license (specified in a LICENSE.txt file in the repository root).
In certain circumstances, we will require a specific license. Usually this will be the BSD 3-clause license. If you’re not sure on a license, check with Casey.
You will maintain a README file describing the purpose and use of the repository.

If you keep your repository private, we will have expectations:

Your repository can be private during development, but expect that one day your code will be world readable.
In the event that you publish a manuscript, we expect that lab members will simultaneously release a code repository capable of generating all of the figures in the paper for which it is appropriate (again, if not sure, ask, but if you wrote code to generate a figure at one point, it should be included).
You will maintain a README file describing the purpose and use of the repository.

We aim to write good code, and we recognize that not all projects are created equal. Using the vocabulary of The Pragmatic Programmer, some code is for production and other code represents tracer bullets. In either case, it’s helpful to use a linter (see tools) and to minimize the number of problematic sections.

Twitter

I'm not going to force you, but most people find Twitter to be a good place for networking and communicating with the broader scientific community. Promoting yourself, and your work, via social media, is important in 2022.

Google Calender

I have a google calender that I'd encourage you to use for notifying me of extended periods of time when you will be out of the office - just send me an email and I can add you to it. If you don't use the calender, I reserve the right to ask you at least daily when you are going to be gone, and where you are when you are away.

Critical Infrastructure

Coffee

• The drip coffee is for everyone.
• If you want to use the French press or Aero press, you need to supply your own coffee.
• If you drink a lot of drip coffee, be a good citizen and buy a bag, on occasion.

Printer

See another member of the lab for the IP address for the printer. You should be able to print things from your laptop/desktop.

Animal Care

If you are going to work with animals, you need to fill out the forms, here: https://www.unh.edu/research/occupational-health-program-animal-handlers.

The Animal Resource Office (ARO) is in the basement of Rudman Hall. Dean Elder is the director.

You'll need card key access to Rudman hall (https://www.unh.edu/research/form/rudman-hall-electronic-access-card-key-request-form), and a metal key to get into the animal area itself.

Equipment

• Tapestation: Get trained before using!! Use for generating size profile fo DNA. There are several different types of tape that you could use.
• Nanodrop and SpeedVac: This is over in the main Genome center lab. Feel free to use.
• The -80C freezer and Ice is on the 5th floor.
• The TissueRuptor and QiaCube are in Gregg 207. Genome center Jeff can train you on these things.
• The Eppendorf robot is availabel for our use. Genome center Steve can train you.

Server

You will likely need access to both XSEDE and Premise.

To set up your premise account:
email [e-mail]
Ask for a premise account with this information:
Full Name:
Email and phone:
Requested login id:
Research Group: MacManes lab
Expected use case / Research area: Evolutionary genomics
ID:

Here's a list of software already install on premise: http://premise.sr.unh.edu/colsa.html#installed-software-packages

Toni Westbrook (office right next to mine) is the COLSA liason for Premise. He is a great resource for all things related to the server, and also Bioinformatics and programming. Ask Toni connect you to the colsa-bigdata slack group for premise updates.

Keys to building, office, lab.

Meet Krys and ask her to submit a key request for you. In addition to the key for the building, grad students wll have keys that open the lab, the conference room, the CABOOSE, and the grad cubes. Postdocs get keys that open every door on the 4th floor. Keys take ~1-2 weeks to get in.

Software and Programming Tools

Code Editors

There are a few editors that are used within the lab listed below. In general, pick something that works for you and learn it well. We recommend an editor that supports linters and other programming-specific capabilities.

• Atom

Manuscript creation

• I tend to write in LaTex. You might want to as well? Try Overleaf (https://www.overleaf.com/)
• If not LaTex, then Google Docs + Paperpile for ref. management.
• Word is fine, but it's nice to be able to edit in real time.. for everybody to be working on the doc at the same time

Publishing

• The lab published manuscripts in bioRxiv.
• The lab publishes exclusively open-access. I pay the premium when applicable.
• Society journals are also to be used when appropriate, with the OA option.
• Our philosopy on Impact Factors is that they are shit. Journal level metrics are inane. There are beautiful papers in the "worst" of journals, and terrible papers in "the best"
• We do not publish in Elsevier-owned journals, given their explicit anti-OA positions.

Reading Material

Science in General

• How To Choose a Good Scientific Problem

Brain Dump

This material will find a home eventually, but will be here for now..

• Label your freezer boxes!!!
• Put everything in paper freezer boxes!
• The fridge is in the genome center. It's the 1st walk-in on the right.
• Seminars are in Rudman and Spaulding. There is a grad student seminar Tuesday and Thursday at 1240. You should attend these if of specific interests, otherwise skip. There is a MCBS seminar 1210-1PM on Friday, that should be more generally intersting. There are also NREN and BIO departmental seminars that are often good.
• The kitchen is for general use. People get upset if you don't clean up after yourself.
• Don't hoard the spoons and forks!!!
• There are bagels, sometimes. Kelley usually brings in. You are welcome to eat, so long as you bring some in on occassion.
• You need a key to get to the 5th floor. It hangs on the lanyard in the lab.

Post-doc specific

• At this stage, assuming you are interested in going to academia, I fully expect that you know you should be publishing a lot. Most competative postdocs are publishing 2-5 1st authored pubs per year.
• I'd love it if you would mentor an undergraduate, and expect you to mentor MacManes lab graduate students.
• I fully expect you to be applying for jobs, and 100% support this effort. You should be looking earlier rather than later, even if you don't feel particularly ready or qualifed.

Grad Student specific

• You will be assigned a cube-space in Gregg. You may or may not use it. People tend to sit in Gregg 420A, but do whatever works for you.
• If you are teaching, these assignments are made by Paul Boiselle, with minimal input from me. You should know a month (ish) before the semester what you will be teaching. You are expected to spend 20 hours per week (MAX!!). Please see me ASAP if you find you are spending more than that.
• Find a committee earlier than not. I can help you brainstorm. Most of you will be in MESB. The handbook can be found here: https://www.dropbox.com/s/faqdpd421binlfq/MESB_handbook_12_18.pdf?dl=0

Acknowledgements

This document was adapted from an onboarding document developed by Casey Green (@GreenScientist).