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<h1>Team Research Lab Handbook</h1> <p>@[toc]</p> <h1>Introduction</h1> <p>Welcome to the Team Research Lab. The Team Research Lab is led by <a href="http://johnpmills.co.uk" rel="nofollow">John Mills</a> and is based out of the School of Sport, Rehabilitation and Exercise Sciences at the University of Essex. Within this handbook you will find details of how I like the group to work and what I expect from you as a lab member. Those who have recently joined the lab are required to read this handbook and those who wish to join are strongly encouraged to do so before applying. Once you have read the handbook, please visit the following <a href="https://forms.gle/W2nKhHLbkumSoH8D7" rel="nofollow">form</a> and sign to say you have read the handbook and agree to abide by the content listed. If you have any questions or comments before signing, please let me know.</p> <h2>Location</h2> <p>We are primarily based in ESA 3.29 of the Sports Arena. Please note that this is a shared space and you will likely spend most of your time working in the Postgraduate office. Where possible, I would like lab members to try to sit together. </p> <h1>Lab member expectations and responsibilities</h1> <h2>Everyone</h2> <h3>Big picture</h3> <p>-Do work that you are proud of. </p> <p>-Do work that others will care about.</p> <p>-Do work that does good.</p> <p>-Double-check your work. Being a little obsessive is essential to good science.</p> <p>-Be supportive of your lab mates. We are a team.</p> <p>-Work independently when you can, ask for help when you need it.</p> <p>-Share your knowledge. Mentorship can take many forms.</p> <p>-Respect each others' strengths, weaknesses, differences, and beliefs.</p> <p>-Science is a marathon, not a sprint. Take personal time/annual leave when you need it and cultivate a life outside of the lab. Respect that other lab members also have a life outside of lab.</p> <p>-Communicate openly and respectfully with other members of the lab.</p> <p>-If you have an issue with another lab member that cannot be solved by talking with them about it, please talk with me. If you have an issue with me, please reach out to Dr Jo Barton as Senior Tutor.</p> <p>-Academia may feel different from other types of jobs, but it is still a job. You should treat working on your research with the same respect that you would treat any other position. See <a href="#hours" rel="nofollow">Hours</a>.</p> <h3>Small picture</h3> <p>-Do not come into the lab if you are sick. Stay home and get healthy, and don't risk getting others sick.</p> <p>-Notify me if you will be out, either due to illness or vacation. Make a note on the lab calendar. If you are sick and you had experiments or meetings scheduled that day, notify your participants or collaborators and reschedule.</p> <p>-You are not expected to come into lab on staff holidays. If you are being paid, then you are expected to come into lab during university breaks (except for staff holidays or if you're taking your paid vacation time).</p> <p>-Keep shared spaces tidy.</p> <p>-The dress code in academia is generally casual. My only request is that you look semi-professional when interacting with participants and when presenting your work. </p> <h4>Undergraduate students</h4> <p>All of the above, plus you will be expected to:</p> <p>-Assist other lab members with data collection or analysis (typically you will be assigned to particular projects).</p> <p>-Work with me or your research mentor to determine your weekly schedule. If you are not able to come in during your normal scheduled time, you must let me know.</p> <p>-Provide extra support to help keep the lab running (this may include filing paperwork). If you are in lab and do not have a task to do, you should ask me or your research mentor whether there is anything you can help out with.</p> <p>-Attend and contribute to lab meetings.</p> <p>-Present at one meeting during the term.</p> <p>-Write a short essay on your research topic or experiences at the end of the term.</p> <h4>M-Level students</h4> <p>All of the above, plus you will be expected to:</p> <p>-Develop a line of dissertation research. Ideally, your dissertation research will consist of at least two cross-sectional studies or one longitudinal intervention that can be packaged into one thesis document.</p> <p>-Apply for external funding. If nothing else, this is an extremely valuable experience.</p> <p>-Do some soul-searching as to what type of career you want to pursue (e.g., academic jobs that are research-focused or teaching-focused, non-academic jobs like data scientist, science writer or project management). We can brainstorm ways of making sure you are getting the training that you need.</p> <p>-Work with a team of undergraduate students. This will speed up data collection and give you some experience with managing and mentoring a team.</p> <p>-Stay up-to-date (and keep me up-to-date) on any deadlines that you need to meet to fulfil departmental requirements (see Time Management).</p> <p>-Prioritise time for research. You may need to take on other work, but it should not detract from your degree. You signed up for a full-time degree and if you cannot meet the obligations that go along with full-time study, you should consider going part-time. </p> <h4>PhD candidates</h4> <p>All of the above, plus you will be expected to:</p> <p>-Develop your own independent line of research. Ideally, your dissertation will consist of at least three experimental chapters that form a coherent thesis.</p> <p>-Mentor undergraduate and graduate students on their research projects, when asked or when appropriate.</p> <p>-Apply for external funding. Applying for external funding is a valuable experience and, if awarded, it will release those dedicated funds for other purposes.</p> <p>-Wait to apply for jobs (academic or industry) until you have completed the data collection component of your Ph.D.</p> <p>-If you are planning to pursue a non-academic career, we can discuss ways of making sure that you are getting the training you need, while still doing excellent research. </p> <p>-Be direct with me and challenge me and the arguments I make. Don’t take my being critical at times of work as an ad hominem attack. </p> <p>-Set high goals that you strive to exceed. I will push you to go beyond what you previously thought possible, but also support you all the way.</p> <h1>Research expectations</h1> <h2>Reproducible research</h2> <p>Reproducible research is research that can be exactly reproduced. This is related to replicability, in that it has to do with your ability to get the same results again, but it refers specifically to getting the same results given the <em>same set of data</em>. I expect that all of our research will be, at minimum, reproducible (I hope that it will also be replicable).</p> <p>Conducting reproducible research is more difficult than it sounds, because it requires that you are organized and possess sufficient foresight to document each step of your research process. There are two main things you can do to improve the reproducibility of your research: (1) extensive note-taking (i.e., as much as you can manage), and (2) programming workflows with version control.</p> <p>Programming workflows help with reproducibility because they take some of the human element out, and in an ideal scenario, you are left with a script or series of scripts that takes data from raw form to final product. Programming alone is not enough, though, because people can easily forget which script changes they made and when. Therefore, all projects that involve programming of any kind (so basically, all projects) must use some form of version control. I strongly recommend git in combination with GitHub (see below), unless you have a pre-existing workflow. This is a hard requirement because a) it is the only way to definitively track the evolution of methods/files over time, b) it allows for easier detection of bugs, c) it facilitates code sharing, and d) it has nice side effects for workflow organization (e.g., thinking in terms of commits, branches, issues). Points a, b, and c are directly relevant to the mission of conducting reproducible research. I am still working towards this ideal myself and will help you as much as I can.</p> <h2>Experiment pre-analysis plans</h2> <p>Most studies undertaken in the lab should be pre-registered or submitted as a Stage 1 Registered Report. This will likely add time on to the front end of a project, but ultimately improves the quality of the final product. There are multiple sites that accept preregistrations including <a href="http://aspredicted.org" rel="nofollow">AsPredicted.org</a> and the <a href="http://osf.io" rel="nofollow">OSF</a>. Here is an example of a recent <a href="https://osf.io/2pbjd" rel="nofollow">preregistration</a> I completed. It is by no means perfect, but it is a start!</p> <h2>Authorship</h2> <p>We will follow APA guidelines with respect to authorship:</p> <blockquote> <p>"Authorship credit should reflect the individual's contribution to the study. An author is considered anyone involved with initial research design, data collection and analysis, manuscript drafting, and final approval. However, the following do not necessarily qualify for authorship: providing funding or resources, mentorship, or contributing research but not helping with the publication itself. The primary author assumes responsibility for the publication, making sure that the data are accurate, that all deserving authors have been credited, that all authors have given their approval to the final draft; and handles responses to inquiries after the manuscript is published."</p> </blockquote> <p>Authorship will be discussed prior to the beginning of a new project, so that expectations are clearly defined. However, changes to authorship may occur over the course of a project if a new person becomes involved or if someone is not fulfilling their planned role. In general, I expect graduate students and PhD candidates will be first authors on publications on which they are the primary lead, and I will be the last author. Whether you or I act as corresponding author will depend on whether you plan to follow a career in academia or not. </p> <h2>Research with humans</h2> <p>Because we are engaged in research with human participants, it is of the <em>utmost importance</em> that we adhere to the School and University's protocols around research ethics. Unless part of a larger project, you will likely require ethical approval for your project, so please consider the University's <a href="https://www.essex.ac.uk/staff/research-governance" rel="nofollow">guidelines</a> with plenty of time. Please note that there are different forms for undergraduate and MSc students. Please also note that you can only apply for ethics once every three weeks. It is your responsibility to manage your time appropriately and to make sure you have completed the forms in time to give me at least one week's notice (preferably two weeks) to review the application. Failing to do this <strong>will</strong> result in your missing the deadline. Please respect my time as I respect yours. If there are any questions about the protocols, or if you're not sure whether we have ethical approval to run your study, please ask me for clarification. </p> <p>If you encounter any problems in the course of doing research that results in a negative outcome for the participant (e.g., if a participant becomes ill or upset, if there is an accident with the equipment, if there is a breach of confidentiality, etc), you should immediately seek assistance from me. If I am not around, you must notify me <em>within 24 hours</em>, preferably as soon as possible. In some cases, we may need to report this information to the university or our funding agencies.</p> <h1>Lab Resources</h1> <h2>Slack</h2> <p>Slack will be used as the primary means of lab communication, such as general lab announcements (<code>#general</code>), sharing links, sharing and/or discussing papers (<code>#papers</code>), and basically any message that can be sent without email. There are also channels specific projects.</p> <p>Try to keep each channel on topic, so that people can subscribe only to the channels that concern them. For messages to one person or a small group of people, use the direct message channels. </p> <p>Full-time lab members should install Slack to their computers and/or phones. Part-time lab members should check Slack regularly. I get Slack updates on my phone and have do-not-disturb mode enabled for evening and night hours (meaning I will not get your messages then); I encourage you to do the same.</p> <h2>OSF</h2> <p>The lab's OSF page should be used as a repository for lab knowledge, particularly as it pertains to ethics, research methods, data, analyses, and documentation of lab procedures/ management. If you learn something new, share it on the OSF page. Each study you run should also be posted to the lab OSF page under a component. I will provide a group tutorial at the start of term.</p> <h2>Google Docs</h2> <p>I encourage lab members to write in Google Docs where possible as it allows for collaborative writing and tracks versions in the cloud. When collaborating on a document, please share the doc by invite via email rather than creating a sharable link as this improves security. Collaborators should be invited to edit the document. However, please select the 'suggest' option in the top right corner when making changes. Should you wish to use different software, please make sure it meets the same requirements as Google Docs (e.g., LaTeX).</p> <h2>Google Calendar</h2> <p>Google Calendar is used to host a general lab calendar <a href="https://calendar.google.com/calendar?cid=YTI3a3ZidmpyNDJnOGcxNnRtN2RtczRpNm9AZ3JvdXAuY2FsZW5kYXIuZ29vZ2xlLmNvbQ" rel="nofollow">TeamResearchLab</a>.</p> <h2>Zotero</h2> <p>I encourage lab members to use Zotero for their reference management. By all using the same system it allows us to easily share resources and hopefully save time. Zotero is open-source software and can be freely downloaded from <a href="http://www.zotero.org" rel="nofollow">www.zotero.org</a>. When conducting literature reviews, I have found a combination of ebscohost and web of science captures the majority of published works. Both websites allow for a more systematic approach to searching, which may be useful down the line. The sites can be accessed at <a href="https://search.ebscohost.com" rel="nofollow">https://search.ebscohost.com</a> and <a href="http://apps.webofknowledge.com/WOS_AdvancedSearch.do" rel="nofollow">http://apps.webofknowledge.com/WOS_AdvancedSearch.do</a></p> <h1>Code of conduct</h1> <h2>General</h2> <p>Many topics were covered already in the <a href="#lab-member-expectations-and-responsibilities" rel="nofollow">Lab member expectations and responsibilities</a> section.</p> <p><strong>In addition:</strong></p> <p>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. Please also see the University of Essex's <a href="https://www1.essex.ac.uk/students/study-resources/documents/2018_School%20of%20Sport,%20Rehabilitation%20and%20Exercise%20Sciences_PGR.pdf" rel="nofollow">Student Charter</a>.</p> <h2>Communication</h2> <p>When communicating in or outside of the lab, I expect lab members to:</p> <p>-communicate within and outside of the lab in a respectful manner</p> <p>-reply to every targeted message (e.g., not newsletters) whenever it is possible</p> <p>-keep their messages as brief and structured as possible</p> <p>-communicate from their professional email account whenever representing the lab. Professional email account is one with institutional affiliation or any other email with their official name in the address.</p> <p>-check their email at least three times per week. -use Slack to communicate when they expect an email chain to consist of more than three replies.</p> <p>-check slack periodically throughout the day.</p> <p>-communicate research achievements, results, and opportunities in a professional manner.</p> <p>-have a professional photograph, biography, and username on social media accounts.</p> <h2>Harassment</h2> <p>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, body size, race, or religion (or lack thereof). We do not tolerate harassment of lab members in any form. Sexual language and imagery is generally not appropriate for any lab venue, including lab meetings, presentations, or discussions.</p> <p>Harassment includes offensive verbal comments related to gender, gender identity and expression, age, sexual orientation, disability, physical appearance, body size, race, religion, 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.</p> <p>Members asked to stop any harassing behaviour are expected to comply immediately.</p> <p>If you are being harassed, notice that someone else is being harassed, or have any other concerns, please contact me immediately. If I am the cause of your concern, then please reach out to Jo Barton who is the School's Senior Tutor.</p> <h1>Time management</h1> <h2>Hours</h2> <p>One of the benefits of a career in academic research is that it is typically more flexible than other kinds of jobs. However, you should still treat it like a job. If you are employed for 40 hours a week, you should be working 40 hours a week. You are not required to work over-time. I do not believe we can achieve much more than around 5 hours of deep work per day and as such, I primarily expect lab members to work towards this goal. However, this really does mean deep, distraction free, and highly focused work! Depending on your status (i.e., full or part-time), I recognise that you may have other demands on your time like training, teaching or other forms of work. For full-time lab members, I expect you to work towards achieving 5 hours of deep work per day. This does, however, leave around 15 hours per week to fit in other commitments, which I think is very fair. Sometimes we will use these 15 hours for lab related activities, so do not book external commitments into this time. I expect that all full-time lab members be on campus between 10am and 4pm, most weekdays. Part-time members should aim to achieve a pro-rata version of the above.</p> <h2>Holiday</h2> <p>Depending on your contract, you will likely be eligible for holiday pay. I fully encourage you to use this time. If you do plan to take a break, please give me a minimum of one week's notice and try to avoid taking time during group projects. When away, please set up an automated out-of-office email that includes the name of someone who can be contacted in case of an urgent matter.</p> <h2>Meetings</h2> <p>I expect members to: -make your calendar open.</p> <p>-attend lab meetings on the second and fourth Monday of each month. The meeting on the fourth Monday of the month will generally be used for breakout activities.</p> <p>-avoid the use of mobile phones or laptops during the meetings (except for taking notes).</p> <p>-avoid eating distracting food (e.g., smelly, noisy etc.) during meetings.</p> <p>-keep meetings brief. </p> <p>-follow an agenda. </p> <p>-start every meeting by stating its (a) aim; (b) agenda; (c) planned duration.</p> <p>-work exclusively on group tasks during two-week sprints.</p> <p>In addition to group meetings, I expect to see students at least once per month on a one-to-one basis. I am available to meet more regularly should you need, but this is the minimum expectation. In general, I expect students to book one-to-one meetings when they feel individual support is required. When booking a meeting, please make sure to create and send through an agenda at least 24-hours before we are due to meet. My calendar is accessible here: <a href="https://calendly.com/jpmillsphd" rel="nofollow">https://calendly.com/jpmillsphd</a></p> <h2>Deadlines</h2> <p>If you need something from me by a particular deadline, please inform me as soon as you are aware of the deadline so that I can allocate my time as efficiently as possible. I will expect at least one week's notice, but I greatly prefer two weeks' notice. I will <em>require</em> two weeks' notice for letters of recommendation. If you do not adhere to these guidelines, I may not be able to meet your deadline. Please note that this applies to reading/ commenting on abstracts, papers, and manuscripts, in addition to filling out paperwork, etc.</p> <h1>Data management</h1> <h2>Storing active datasets</h2> <p>In general, data will be stored in one of two places: - <strong>The lab folder on our secure departmental server</strong> - Data to store here: consent forms, keys to subject IDs (identifiable data ok) - <strong><a href="https://osf.io/tv2uh/" rel="nofollow">OSF</a></strong> - Data to store here: aggregated datasets (no identifiable data!!!)</p> <p>In general, you should only store data locally on your computer when running analyses. Once finished, you should add the analyses and relevant scripts to the relevant server and delete from your computer.</p> <h2>Data organisation</h2> <p>My OSF project components typically look something like this: - <code>Pre-Data Report</code> - This typically includes your introduction and methods - <code>Measures and methods</code> - This typically contains documents that explain what measures and methods you have used. This may be original questionnaires and scoring keys, and any composite surveys you have created. Stimuli and presentation scripts may also be included here. - <code>Data</code> - This typically contains all your aggregated data. Most of what I do is anonymous at source and can be included. Identifiable documents (e.g., with a name and signature) should not. - <code>Analyses</code> - This typically contains the scripts from your data analyses. Reviewers should be able to reproduce what you have done. Please use the wiki to describe your process where required. - <code>Post-Data Report</code> - This is typically the completed manuscript that you have preprinted/submitted for publication. All revisions should be stored in this folder too and the wiki utilised to explain changes.</p> <p><strong>Please note that components should be set to private as default. Should you wish to make the contents publicly available, please check with me first.</strong> </p> <h2>Archiving inactive datasets</h2> <p>Before you leave the lab, you will be required to document and archive any dataset that you have collected. I will review the dataset with you before you leave. [To add: information about where to archive data]. </p> <h2>Data sharing</h2> <p>Not only is data-sharing the right thing to do, we are actually required to do so for any dataset that was funded by certain funding agencies. We will make these datasets publicly available within a year of publishing the first paper from the dataset. You should also be prepared to share any scripts that you used in your published processing & analysis pipeline. Please note that data collected via financial support from the lab, must stay in the lab until the funding agency requirements are met. This is to protect the funders who have paid for the data to be collected.</p> <h1>Funding</h1> <p>Funding for the lab comes from:</p> <p>-<a href="https://www.wada-ama.org/" rel="nofollow">World Anti-Doping Agency</a></p> <p>-<a href="https://www.thebritishacademy.ac.uk/" rel="nofollow">British Academy</a></p> <p>-<a href="https://www.leverhulme.ac.uk/" rel="nofollow">Leverhulme</a></p> <h2>Lab member budgets</h2> <p>Lab members studying for a PhD will typically have access to a budget of around £2,500 assigned to them. This can be used for training and conference travel. At present, a maximum of £700 can be spent on conference travel. There are also discretionary funds within the school we may be able to access to support your development. I also try to pay for M-Level students to attend one conference during their first year in lab. Most of the latter is generated via external grant income and is only available if we are successful in grant applications. I will always try to help lab members out where I can and expect members to apply for grants (e.g., travel, seed etc.) to help contribute where possible.</p> <h2>WADA funding notes</h2> <p>When sharing information regarding research funded by WADA, it <em>must</em> include the following statement 'This project has been carried out with the support of the World Anti-Doping Agency'. This is essential for documenting that we are turning their money into research findings. We must also submit a yearly progress report describing what we have accomplished. Lab members involved in the research will be asked to contribute to the progress report.</p> <h1>Training</h1> <p>The University of Essex provides access to a range of optional training for Postgraduate students via Proficio. You can access details of this via Moodle and searching for PGR information.</p> <p>The following three courses are also considered core training for the lab:</p> <p><a href="https://www.coursera.org/learn/statistical-inferences" rel="nofollow">https://www.coursera.org/learn/statistical-inferences</a> <a href="https://www.coursera.org/learn/sciwrite" rel="nofollow">https://www.coursera.org/learn/sciwrite</a> <a href="https://www.youtube.com/watch?v=4WVelCswXo4" rel="nofollow">https://www.youtube.com/watch?v=4WVelCswXo4</a> and materials <a href="https://github.com/rmcelreath/statrethinking_winter2019" rel="nofollow">https://github.com/rmcelreath/statrethinking_winter2019</a></p> <p>I expect full-time PhD candidates to have completed this training within their first six-months of joining the lab. Part-time PhDs should look to complete all three within their first year. Full-time MSc and MSD candidates are expected to complete Kristin Sainani's course and one of the two statistics focused courses (your choice) within their first six-months. Part-time MSc and MSD candidates can discuss specific needs with me. Although I do not make it a requirement that undergraduates who wish to join the lab complete some or all of this training, preference will be given to applicants who have.</p> <h1>Undergraduate or taught Masters research</h1> <p>Undergraduate and taught Masters research assistants play an important role in our lab, and we have a few opportunities for them to earn money or credit for their contributions. Because these opportunities require a certain degree of commitment from both the student and the lab, we generally reserve them for students who have already spent at least one term volunteering in lab. If this policy would prevent you from being able to work in lab, please talk to me because we want all students to be able to pursue their research interests.</p> <p>In addition to volunteering in lab, other research opportunities include: 1. If you are and undergraduate student, want to work in the lab, and earn research credit, you can sign up for independent study or undergraduate research (<a href="mailto:john.mills@essex.ac.uk">email me for info</a>). We will have to fill out a syllabus contract at the beginning of the term. Typically you would be in lab for 6 hours a week, and you would also be required to attend lab meetings, present at one of them, and write a short statement about your experiences at the end of the term (this typically forms the basis of your assessment in SE201). 2. If you are an undergraduate student who wants to work in lab and earn money, you can apply for an <a href="https://www1.essex.ac.uk/urop/" rel="nofollow">Undergraduate Research Opportunities Programme</a>. Candidates are expected to be academically strong (typically, attaining &gt;60 the majority of their modules) and are expected to work 10 hours per week. Because these fellowships are intended to support your academic development, UROP students will be strongly encouraged to participate in lab meetings. The benefits are quite good and opportunities competitive, so please let me know with plenty of time if you wish to apply. 3. If you want to work in lab, earn money, and are eligible for work-study, there may be other paid research opportunities available.</p> <p>If you're an undergraduate or taught masters student and you want to pursue any of these options, please talk to me. The more notice you give, the higher the likelihood of obtaining a positive outcome.</p> <h1>Recommendation letters</h1> <p>Letters of recommendation are one of the many benefits of working in a research lab. I will write a letter for any student or lab member who has spent at least one year in the lab. Letters will be provided for shorter-term lab members in exceptional circumstances (e.g., new lab members who are applying for fellowships). I maintain this policy because I do not think that I can adequately evaluate someone who has been around for less than a year.</p> <p>To request a letter of recommendation, please adhere to the deadline requirements described above. Send me your current CV and any relevant instructions for the contents of the letter. If you are applying for a grant, send me your specific aims or a short summary of the grant. In some but not all cases, I may ask you to draft a letter, which I will then revise to be consistent with my evaluation. This will ensure that I do not miss any details about your work that you think are relevant to the position you're applying for, and it will also help me complete the letter in a timely fashion.</p> <h1>FAQ and who to ask</h1> <p>TBD. Ask me some questions.</p> <h1>Sources</h1> <p>This handbook was inspired by <a href="http://jpeelle.net/peellelab_manual.pdf" rel="nofollow">similar</a> <a href="https://github.com/memobc/memolab-manual" rel="nofollow">handbooks</a> and in some places <a href="http://ivory.idyll.org/lab/coc.html" rel="nofollow">(e.g., here)</a> I have adapted or reproduced content verbatim. The contents of this handbook and of those I have adapted or reproduced is licensed under a <a href="http://creativecommons.org/licenses/by/4.0/" rel="nofollow">CC Attribution 4.0 license</a>. Thanks are given to those scholars for laying the foundations and making the production of this handbook a much simpler task.</p>
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