0000-0002-5974-6523
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trife
Clemson University
This manuscript (permalink) was automatically generated from RifeLab/lab-manual@aae71a3 on January 31, 2025.
0000-0002-5974-6523
·
trife
We’re happy you’ve decided to join the Rife Lab at Clemson University. We’re really glad to have you as a team member and will do what we can to make your time in the lab amazing. We hope you’ll learn a lot about plant breeding, develop new skills (coding, data analysis, writing, giving talks), make new friends, and have a great deal of fun throughout the whole process.
This manual was developed by me, Trevor Rife, to provide a structured vision for how the lab should function and to complement existing Clemson University policies (which take precedence). When you join the lab, you’re expected to read this manual and sign a form indicating that you have done so. You’re also highly encouraged to read it while deciding if you want to join the lab in the first place. You should always feel free to talk to Trevor for clarity about anything in the lab manual or to suggest improvements.
The Rife lab seeks to develop, validate, and implement new tools and technologies into breeding programs around the globe. Using these tools, we aim to better understand the genetic control of economically important traits in crops that are regionally relevant for the Southeastern United States. Critical to this goal is training the next generation of scientists, creating a safe and inclusive space for research, and facilitating an open and collaborative environment that promotes scientific advancement.
This manual was adapted from other lab manuals developed by Casey Greene, Jenna Hershberger, Mariam Aly, Jeffrey Ross-Ibara, Jonathan Peelle, Valerio Hoyos-Villegas, Erin Sparks, Amanda Hulse-Kemp, and Jean-Luc Jannink. This version is distributed under a CC-BY 4.0 License.
The repository for this manual is on GitHub. To propose changes: fork the repository, edit the files you wish, create a pull request, and assign Trevor to review the changes.
All members of the lab, including visitors, are expected to follow this code of conduct. We expect cooperation from all members to help ensure a safe environment for everyone.
The lab is dedicated to providing a harassment-free experience for everyone.
We do not tolerate harassment of lab members in any form.
The lab is committed to ensuring a safe, friendly, and accepting environment for everybody. We will not tolerate any verbal or physical harassment or discrimination on the basis of gender, gender identity and expression, sexual orientation, disability, physical appearance, body size, race, or religion. We will not tolerate intimidation, stalking, following, unwanted photography or video recording, sustained disruption of talks or other events, inappropriate physical contact, and unwelcome sexual attention. Members asked to stop any harassing behavior are expected to comply immediately. Sexual language and imagery is generally not appropriate for any lab venue, including lab meetings, presentations, or discussions.
If you are being harassed, notice that someone else is being harassed, or have any other concerns, please contact Trevor immediately. If Trevor is the cause of your concern, talk with one of the other members of the PDREC administrative staff. For official concerns, please see the Clemson University ombuds office.
You are expected to be respectful, tolerant, and non-discriminatory towards your colleagues both in the lab and at the university. We adhere to all university policies on harassment and discrimination. I expect lab members to contribute to a productive and friendly environment conducive to learning and research. This includes treating your colleagues with respect, listening to others’ viewpoints and ideas, and ensuring the lab is a place where everybody feels welcome and appreciated.
All members of the Rife lab are expected to conduct research with the highest standard of rigor and integrity while upholding Clemson’s Standards of Ethical Conduct.
You have a responsibility to me, the institutions that support our work, and the broader scientific community to maintain the highest standards of scientific accuracy and integrity while being a faithful steward of state and federal grant funds. By being in the lab, you agree to adhere to professional ethical standards including accurate documentation of experimental design, results, and interpretation in a lab notebook. You are obligated to be honest, trustworthy, and transparent in your scientific research.
It is also important that you prioritize the accuracy of your work. Unintentional errors due to inattentiveness or rushing can be extremely damaging and produce results that turn out to be incorrect. It is critical that experiments are designed to minimize error and maximize quality results. Please double-check your work frequently and don’t hesitate to ask a colleague to look over a dataset or analysis.
If you have any questions, or in the unlikely event that you have concerns about a research practice you have seen in the lab, please talk to me immediately. If you are feeling pressured to succeed (publish a lot, publish in high impact journals, etc.), you should reach out to Trevor to discuss. This pressure is something we all face but is never an excuse for research misconduct.
The Rife Lab is committed to ensuring research integrity and we take a hard line on research misconduct. We will not tolerate plagiarism, fabrication, or falsification. These activities are unacceptable in any form, whether as part of course work or research activities. Plagiarism and falsifying information have severe consequences including course failure, possible firing, or dismissal from the degree program. Research misconduct is a disservice to you and risks your entire career. It is never right and never worth it. Don’t do it.
From the Clemson University Academic Integrity Policy:
“Plagiarism, which includes the intentional or unintentional copying of language, structure, or ideas of another and attributing the work to one’s own efforts” is absolutely not allowed, whether as part of course work or research activities.”
From the Graduate School Policy handbook: > “Fabricating or falsifying information involves actions such as making up data that were not collected, stating that studies were conducted that were not, indicating that original source material was read when information was obtained from secondary or tertiary sources, making up references not used, or identifying sources that were not consulted (e.g., telephone interviews).”
Your health and safety are more important than your research and require adhering to lab safety codes. Never work in the lab if you are feeling sick, under medication that might affect your ability to work normally, or are under the effects of any kind of drug. Avoid working in the lab by yourself doing potentially dangerous activities, and please be aware of Clemson resources and training on lab safety.
All lab members are expected to comply with University, REC, and lab safety protocols. All lab members are must undergo mandatory comprehensive safety training for lab and pesticide safety. Lab safety and other trainings will be presented online via TigerTraining or Bioraft/Scishield. Contact Sara Pederson to schedule your pesticide safety training. Information specific to the Pee Dee REC can be found on the REC website
SDS are an excellent source of information on the health and physical hazards of chemicals. SDS should always be reviewed before using a new chemical. Our SDSs are located in (todo). When a new chemical is purchased, the ordering party is responsible for adding the SDS into our collection.
New lab members may request a lab coat if necessary for your research. When performing experiments, members should wear closed toe shoes, long pants, and should tie back long hair.
In case of injury, it is an employee’s responsibility to notify his/her supervisor or department head immediately. Any injury, no matter how slight, must be reported to Trevor. Follow the injury or accident reporting procedures. There are separate forms that must be filled out depending on whether or not medical treatment was required.
Hurricane season is June 1 - November 30. In the event of a tropical storm or hurricane, please follow state, university, and PDREC guidelines.
Loss of power is common at PDREC during storms. There is a generator for the building, but it occasionally fails. In the event of power loss while you’re workign in the lab, unplug hot plates or other equipment and store in-progress samples if possible and safe. Do not open any fridges or freezers if the power is off.
You are ultimately responsible 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 and contribute to a healthy and productive research environment. When disagreements about methodological approaches arise, you recognize that these should be resolved through a solid and reproducible analysis of available data. If you aren’t sure — ask. Members are expected to behave respectfully, ethically, professionally and safely while working within and outside the research group. Mistreatment will not be tolerated.
Flexible working hours are a big benefit to working in an academic lab. My primary concern is that you get your work done in order to complete both individual and group goals. To promote communication and interaction, lab members are generally expected to be present (or remotely available) for the majority of normal business hours (9am-5pm, Monday-Friday), since this is when most academic activities occur. However, I expect members to set a schedule for them that best facilitates their productivity and personal happiness. Note that you may need to adjust your hours to complete specific tasks or work with partners (e.g., the PDREC farm crew works from 7am-3pm, meeting with international collaborators on projects, etc.). Your schedule should include time to attend weekly lab and one-on-one meetings. You are not expected to regularly work more than a normal 40-hour work week.
There may be rare times when your project requires working late at night or on the weekends. If you are in lab by yourself on the evenings or weekends, make sure that someone (the PI, other lab members, or a family member) knows that you are there. This is for your safety and the safety of others.
I am generally available during the work day and prioritize answering Slack messages. I am usually unavailable during the weekend, so ensure that I’m aware of any impending deadlines. I will occassionally send emails or Slack messages outside of normal working hours–I do not expect you to respond to any messages outside of normal working hours. If off-hours messages are unwelcome, please let me know. In case of emergencies, contact me by cell phone at any time.
Work from whatever location best facilitates your ability to complete the duties of your job and supports your productivity. There is no limit on work remote, as long as you are making satisfactory progress towards mutually agreed upon goals as determined by you and Trevor. However, you are encouraged to make time for regular in-person interactions with lab members and department colleagues.
These guidelines are intended to cover logistics for planned time off (2+ days in duration).
All full-time Rife Lab members are encouraged to take up to 15 days of vacation each year in addition to the 13 days of official University holiday (Martin Luther King Jr. Day, Memorial Day, Independence Day, Labor Day, Election Day, Thanksgiving (2 days), Winter break (6 days)).
Reproducible research is an essential part of science, and an expectation for all projects in the lab. Individuals unrelated to your research should be able to reproduce your results from your raw data and scripts. Experimental design, analysis scripts, and pipelines should be well-documented and organized with extensive notes for each step. An organized physical or electronic lab notebook is required to help document how and in what order activities were performed (pre-processing data, running models, statistical tests). It is highly encouraged that you use version control (e.g., Git in combination with GitHub) to manage project development, facilitate long-term maintenance, and simplify code sharing. The lab’s GitHub is https://github.com/RifeLab and new repositories can be created to host specific projects.
Organization is vital to maintaining sanity in academia. Disorganization and procrastination hurt you, your collaborators, and people whose help you need. Collaborators should be notified as soon as a deadline is known. It is appropriate and appreciated to remind collaborators (including Trevor) as deadlines get closer.
Letters of recommendation are extremely important for getting new positions and grants. With exceptions, I will generally only write letters if you have been in the lab for at least one year. If you need a letter, notify me as soon as possible with the deadline, your CV, and relevant instructions for the content of the letter. If the letter is for a grant, include your specific aims. If the letter is for a faculty position, include your research and teaching statements. In many cases, you may also be asked to submit a draft of a letter, which will be extensively modified, made more glamorous, and edited to add anything important that you left out. While this process will likely feel awkward, it ensures that the letter contains all the information you need, and that it can be submitted on time.
The Rife Lab is responsible for a state-owned Tahoe to be used to complete research and field activities. In order to drive state vehicles, you are required to take an online training course. The mileage log must be filled out whenever the Tahoe is used and turned in monthly. Blank logs are available in the mail room. For state vehicles, gas can be pumped on station. There is a small receipt book kept near the gas tank where you can record your name, date, tag number, and number of gallons pumped. If you have any questions about the gas key you should contact Sam. The fuel card must be used for off-station fuel, along with a special PIN. Contact Jenifer Lind if you believe you will need a PIN to get fuel.
Ensuring that lab members get along and want to spend time with one another is a critical aspect to developing a productive, friendly, and positive lab environment. But I also realize that you are all very busy and want to have a place to focus and work quietly. While we do not have specific quiet time hours, please respect other people’s needs to work quietly in labs and offices. If someone is wearing headphones, respect their desire for isolation (with obvious exceptions for emergencies). If you required additional quiet or privacy for specific work or projects, feel free to work from home, a library, or anywhere else.
If a student or postdoc collects a dataset but does not completely analyze it or write it up within 2 years after the end of data collection, the project will be re-assigned to another person to expedite publication. If a student or postdoc voluntarily relinquishes their rights to the project prior to the 2-year window, Trevor will also re-assign the project. This policy ensures that data and results are published but ensures priority is given to the person who initially collected the data.
Intellectual Property guidelines are handled in accordance with the instructions from our research sponsors and university guidance. Lab members must follow the Clemson Participation Agreement and the agreements with our sponsors. These often allow, encourage, or require openness. If you have concerns at any point, set up a meeting with Trevor to discuss these concerns.
Files shared over Slack or Email should include dates in the name using the YYYYMMDD format.
Graduate students in the lab will:
In turn, Trevor will:
PES does not have a required course list, however, your individual advisory committee may require specific courses for you. Keep in mind that Graduate assistants are limited to 12 credits per semester. The following requirements must be met through your planned course of study:
Masters:
PhD:
Every graduate student is required to have a graduate committee made up of graduate faculty members, with at least half being from PES. Masters students must have a minimum of three faculty members on their committee and the committee must be formed no later than the middle of their second semester. PhD students are required to have a mimimum of four members, and their committee must be formed by the beginning of the fourth semester of their doctoral program.
Graduate students will interact with their advisory committees regularly. Students should consult the graduate student handbook and/or correspond with the coordinator for their graduate program (Guido Schnabel) to understand the expectations that exist around communication with committee members. Questions around what document(s) their committee will expect to see and when they should be sent to the committee should be resolved with the committee at least a month in advance of a scheduled meeting. Students in the Rife Lab are not to provide food or drinks for committee members.
The comprehensive exam is designed to evaluate your overall mastery of a body of knowledge and skills after completing most of the program of study. Satisfactory completion of the comprehensive examination must occur at least six months before graduation. The advisory committee meets with the student and sets the details and rules for the examination. Written examinations should be evaluated and returned to the student with appropriate comments before the oral examination. The oral examination will include questions covering areas where weakness was demonstrated on the written examinations. Oral exams typically last 2 to 3 hours.
Both the PES department and the PDREC have active graduate student associations. All graduate students are strongly encouraged to participate in these groups.
If you are interested in staying in the graduate student housing at the PDREC, please contact both Mandy Stephan and Trevor.
When in doubt about any specific policies, consult the graduate school policy handbook and the PES graduate program handbook.
CCIT provides several guides and information for incoming students and new faculty and staff. For the Rife Lab, members are expected to have accounts or sign up for the following:
The Rife lab uses the Advanced Plant Technology Slack Workspace as the primary tool for internal communication. The best way to get in touch with Trevor is via a direct message in Slack. Full-time lab members should install Slack on their computers and/or phones; part-time lab members should check Slack regularly. 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, use direct messages. If you have to send messages that include out-of-lab recipients, use e-mail. You should feel free to ignore Slack on evenings and weekends.
The Rife Lab maintains a shared OneNote notebook. Each lab member has a separate section that will be used to track weekly progress between meetings. These sections are self-managed by lab members but are generally structured with each weekly meeting being a separate notebook page. Each week before your individual meeting, you are expected to add a page to your section and document your progress during the last week, goals for the next week, and any questions related to your projects. While much of the content of these pages will be text, images, graphs, and other media are often helpful to include. If Trevor is unable to attend the individual meeting, he’ll annotate your page in red to give feedback.
The Rife Lab uses GitHub to store and share code and data with the world.
The lab has a shared calendars with activities relevant for the entire lab. This calendar is used to keep track of lab events, lab meetings, travel schedules, and birthdays.
The lab has a shared Box folder that is used to store large amounts of experimental data. The lab Box is also used to store documents and files for general lab use. Lab members have a subdirectory in the Rife Lab Box share that should be organized by project.
New lab members are responsible for supplying Trevor with a photo and writing a blurb about themselves for the lab website. These pages can be updated (or created) by members by forking the repository, making changes, and creating a pull request.
Lab members are provided with a computer by request. Please discuss your project’s computing needs with Trevor to best optimize resource usage. For interns and undergraduate students, these machines may be shared. For full time lab members, the operating system should be reinstalled when a new member joins.
Lab members will be provided with the necessary hardware to complete their work. You are responsible for letting Trevor know what you need, including uninterruptable power supplies, external monitors, peripherals, and office furniture (e.g., desk, chair, etc.)
A key to the Pitner Center will be provided to each lab member. If required, a key to the lab pesticide cage will also be provided. It is the responsibility of each lab member to keep track of their keys for the security of everyone at the PDREC. Do not share your keys or let anyone borrow them.
Every PDREC employee is provided with a unique code to the front gate. Do not share your gate code with anyone. If you forget your gate code, talk to Mandy. If you are hosting a visitor who will be arriving separately, let Mandy know when to expect them and either meet them at the gate or give them driving instructions to the front of the Pitner Center.
Maintenance requests and Greenhouse reqeusts can be created by submitting a work order request form. Discuss with Trevor before submitting to determine specifics for the request. Mandy receives all of the request submissions and forwards them to the REC director and facilities lead (Sam Goodman). Please keep this in mind when writing your request and ask nicely!
I attempt to meet individually with all lab members for about an hour each week. The goal of the weekly meeting is to discuss research challenges and plan strategy. Individual meetings can be in person or via Zoom–bring your computer if the meeting is in person. You are responsible for updating OneNote prior to the meeting with what you accomplished over the last week and what tasks you aim to complete by the next week. A product of the meeting is a list of what you want to do before the next meeting. By default, I do not reschedule individual meetings due to scheduling conflicts, but I will annotate your OneNote page to answer any questions or provide insights.
The Rife Lab holds a joint weekly lab meeting with the Hershberger Lab at PDREC. Weekly lab meetings (~1 hour) are meant to be a forum for trainees to present project ideas and/or data to get feedback from the rest of the group. Each lab member is expected to present at lab meeting at least once every semester. These meetings are informal, and you can do what you wish with your slot – just be prepared to contribute something substantive. Projects at any level of completion can benefit from being presented. Lab meetings can also be used to talk about methods, statistical analyses, new papers, career development, or as an opportunity to prepare for conference presentations and give people feedback on job talks or other external presentations. Lab members are expected to attend every meeting (barring excused absences due to illnesses, doctor appointments, family issues, etc.).
The Rife Lab holds a weekly developer meeting (~1 hour). These meetings serve as a forum to discuss upcoming changes to software being developed in the lab. Developers are limited to 10m to discuss what they are working on, give quick demos, and solicit feedback from participants. The second half of these meetings are an opportunity to provide support to external users or research groups that join the meeting. All developers are expected to attend and participate in every meeting (barring excused absences due to illnesses, doctor appointments, family issues, etc.).
Journal club is an opportunity for lab members to strengthen their ability to comprehend and critically analyze published research. For these meetings, lab members are expected to read an assigned paper and attend with comments and questions about the reserach. Let Trevor know if you have a specific topic or paper that you’re interested in discussing at lab meeting.
Requesting items for purchase in the Rife Lab is done via GitHub.
In the Orders repository, create an issue following the provided template.
Account numbers can be obtained in the lab-info repository.
Once the order is created, assign the issue to Trevor.
Trevor will attach a receipt to the issue once the item has been ordered.
You are responsible for closing the issue once the item has been received.
If an order totals under $2,500, it may be purchased via PCard If an order is over $2,500, it must be purchased via Buyways. If over $10,000, multiple quotes must be obtained (unless it is a sole source purchase). Clemson is only tax exempt for agriculture-related purchases. Ask Jenifer Lind for a agricultural tax exemption card if you will be making this type of purchase. See the Clemson Procurement Guidelines for more information.
PCard puchases must only be made for allowable items (Notable expenses that are not allowable include hotels, meals, gas.). See the PCard Policy for a full breakdown of allowable purchases. If you use the PCard for a purchase, you are responsible for getting the receipt to Trevor. Failure to follow PCard guidelines may result in losing PCard privileges.
Amazon is a common vendor used by the lab. All Amazon purchases must be made by Trevor through the lab Amazon Business account. The PCard cannot be used in non-business accounts and no personal Amazon accounts should be used for lab procurement.
The delivery address for PDREC is:
Clemson Pee Dee Research & Education Center
2200 Pocket Rd
Florence, SC 29506 Purchases made on behalf of the lab can be reimbursed through Concur. Reimbursement requires proper documentation including the purchase receipt. Purchases should not be made without prior approval.
Experiments should be designed to be easily analyzed, control error, and give reasonable assurance that the differences between treatments will be detected. For general breeding experiments, Trevor will provide a trial layout file one month before the planting date. Reproducible R scripts (with set seeds) should be used to design your field experiments. Write out the statistical model you will use to analyze your data when you are designing your experiment. When in doubt, consult a statistician.
Land use at the PDREC is allocated by the Land Use Committee, which includes the station Director, Farm Manager, and three resident faculty and/or extension associates. If you need land for an experiment, let Trevor know as soon as possible.
Required details include:
Land use decisions are made at the beginning of the calendar year, so if we do not request land at that time, we cannot be guaranteed space. Fields are assigned by the PDREC Land Use Committee. Irrigated fields must be requested using the PDREC Land Use form approximately seven months before desired planting date.
The PDREC farm crew will assist individual projects with field preparation, planting, and maintenance. The farm crew will help as needed, but do not expect the farm crew to perform data collection for you. The farm crew works from ~7am-3pm ET, so plan accordingly if you need assistance with your field experiments.
Decide on the phenotypes to capture as the experiment is being designed. Use public ontologies to select traits and follow the methods described there to capture the phenotypes. Do not create your own method unless you have double checked that existing methods do not meet your needs. Be consistent with phenotyping methods within the lab and especially within a field trial. Inconsistency can compromise the validity of your results.
We use Field Book for all phenotyping in the lab. The lab will provide Android phones or tablets for data collection, but you are in charge of keeping track of your tablet and making sure it is charging when you leave for the day. Do not collect phenotype notes on paper. Consult the official Field book documentation to learn about the app and various features available. In most cases, date, numeric, boolean, and categorical trait types can capture the information needed but text traits should be avoided since they can be difficult to analyze. If you find a bug in the app, report it by creating an issue on GitHub.
To increase throughput and minimize mistakes, barcodes are used throughout the breeding program in the Rife Lab. Barcode labels can be prepared with Bartender software. When preparing barcoded labels for your germplasm or plants, you should use one of the defined templates to ensure continuity in the lab. These templates should not be edited by students or postdocs. For field activities, two sets of labels should be printed: a poly one for stakes and a paper one for seed envelopes.
You are responsible for taking care of your plants. You must be trained before using the soil mixer. Jonathan K Windham is the greenhouse manager and should be contacted for greenhouse questions or clarifications.
Germplasm is stored in the cooler in the field lab. If you are performing an experiment and determine there is insufficinet source seed avaialable, contact Trevor and do not use all of the remaining seeds. Keep the cooler door shut when not moving seed between rooms.
All code from the lab should be well-documented and maintained under version control and will be shared along with data for all lab manuscripts. All analyses should be entirely reproducible and well-documented in the form of makefiles, shell scripts, or other automation approaches that allow analyses to be automatically performed. These scripts, including those to generate figures will be included in repositories (see “Getting Code into RifeLab Repositories”) and made publicly available with a preprint or manuscript submission. Depending on the application, we write code Kotlin, Java, R, or Python; code for visualization should be in be Python or R.
Our primary version control service is GitHub, and we have an organization called RifeLab there.
Lab members are expected to maintain their code in repositories within the RifeLab organization.
When you join the lab, a repo with your name will be created and used as long-term storage for your research outputs.
Project-specific repositories should be created to organize project files, simplify the process of reproducibility, and serve as a means of publishing analyses.
Contributions to project respositories should be made using pull requests to facilitate code review (see below).
RifeLab repository through pull requests (see below).Code moves from user repositories to RifeLab repositories through a process of code review that is handled through pull requests.
The process is described briefly below.
Feel free to ask for guidance if you are uncomfortable with the process.
We will revoke write access for failing to adhere to these rules.
RifeLab.lab-manual) where, in addition to the above rules, Trevor must also approve the pull request.Each pull request may contain one or more changesets. In keeping with good source control practice, each changeset or commit should contain all changes necessary for a particular fix or update. In addition, each pull request should relate to no more than one functional area in the code base you are updating. Keeping the pull request focused to one area makes it easier for your reviewers to provide thoughtful feedback.
All lab members are expected to participate in code review when it matches your expertise. If you get named by the submitter, it’s courteous to review the request. A checklist is available to help facilitate and guide code review. As a reviewer, you are responsible for making sure that all checklist guidelines are followed.
Some repositories will contain project failures (e.g. proof-of-concepts that didn’t work). This is ideal. Being able to find them will make sure we don’t make the same failure twice.
Non-code documents should be kept in a place that maintains version history. Clemson provides Box for these purposes.
We release as many research outputs as possible under permissive open licenses to ensure our research is reusable and reproducible with minimal legal barriers. The default license for software that should be applied to new lab related repositories is the GPL 3. In certain cases, a funding agency or other upstream restrictions may require alternative licensing.
All code written by lab members should be appropriately commented to ensure others can understand the functionality and help when debugging issues.
Data management is the process of collecting, storing, organizing, and maintaining data in a structured and systematic manner to ensure its availability, accuracy, and usability. The Rife Lab strives to organize and store data efficiently and effectively to maximize utility. Members of the Rife Lab involved in data collected should implement principles of the Data Lifecycle.
A Data Management Plan is a formal document outlining how data will be handled during and after research. It is often required for grant proposals, and is helpful to consider when starting a project to ensure you have the ability to manage all data types that will be collected. A good DMP will include considerations for data types, collection methods, data formats, how the data will be used, how the data will be shared, and expected data volume.
Collection method directly impacts impacts the data format, accuracy, and collection throughput. Data should be machine readible to simplify analysis including using flat files with plain text, descriptive headers, limited spaces and special characters, and consistent data types. Capturing metadata facilitates reuse and provenance and helps make the data meaningful.
A copy of raw data should always be maintained in an unmodified state. All changes to a dataset via scripting should be recorded via version control (Git). Modified data files should be saved under a new name (don’t overwrite the original). Outlier removal should be standardized, reproducible, and statistically justified.
Your analysis should be entirely reproducible by independent scientists outside of the lab. A consistent scripting language should be coupled with comprehensive documentation (e.g., code comments, a repo readme, software versions used, etc.). Reproducibility increases transparency and credibility and helps you remember what you did when it comes time to write and publish your projects. R markdown, Quarto, and Jupyter Notebook are all great tools to help make your analysis documentation easier. They allow for a mix of text and code and output nice PDF or HTML documents.
Data is often irreplaceable and efforts should be made to ensure it doesn’t become inaccessible or lost.
Raw data should be stored in non-proprietary, future-proof file formats when possible.
Full-time employees should regularly back up their computers on an external drive, preferably through an automated backup program.
Raw data should include a README file that includes all necessary guides and metadata necessary to understand and utilize the data.
Files should be organized using a consistent and logical directory structure.
Project management such as the R package workflowr can be used to create a backbone directory structure automatically.
In the Rife Lab, scripts scripts and small data sets should be stored in project-specific repositories on GitHub.
Large datasets should be stored on the lab NAS server or in the lab Box directory.
ALWAYS CHECK WITH TREVOR BEFORE SHARING DATA! Open science is an approach to conducting scientific research that emphasizes transparency, accessibility, collaboration, reproducibility, and inclusivity. The Rife lab supports open science and is committed to publishing preprints and making all data and code public upon publication. Sharing data requires understanding who is responsible for the data and has the right to make decisions about access. Unless told otherwise, data can be shared within the research group without explicit permission. Prior to publication, data may be shared among collaborators giving them access, often with the understanding that they will allow the data creator to lead the publication effort. Copyright is typically held by the creator of the data. Licenses specify how data can be used, shared, and redistributed and can be applied to data, code, and written word. Data should always be shared according to funding agency requirements. It is Trevor’s responsibility to make the final decision regarding data sharing.
The FAIR principles are a set of guidelines to help improve the Finability, Accessibiliy, Interoperability, and Reuse of digital assets (Wilkinson et al., 2016). As a member of the Rife Lab, you are expected to familiarize yourself with these principles via the FAIR website and put them into practice.
Written communication skills are one of the most important skills in academia. Graduate students and postdocs are expected to draft their own manuscripts and work with Trevor to make iterative revisions. In the Rife Lab, a citation manager is required for all manuscripts. Examples of citation managers include Zotero (preferred), Mendeley, Endnote, Paperpile, etc.
When naming offline files to send to Trevor or external collaboratorss, include your name and a date in the filename (e.g., hersh_cv_20240917.docx).
I will generally append my initials to file names after making comments (e.g., hersh_cv_20240917_twr).
Once you have incorporated changes, the file can be renamed with the current date before sending for comment.
Draft manuscripts are required to have the following:
Any of the above formatting can be modified prior to journal submission, but these formatting guidelines should be followed to facilitate consistent internal formatting and simplify revisions.
Draft manuscripts should be free of most spelling and grammatical errors–especially prior to sending out to collaborators. Scientific manuscripts should generally be written entirely in the past tense. Lab members are available to help proofread and explain why certain words or phrases should be used. Reading manuscripts out loud to yourself is a good approach to catch sentences with missing words, grammatical mistakes, or sentences with subject-verb disagreement. Manuscripts with copious amounts of grammatical errors or sloppy writing may be returned to you without being reviewed.
When writing, do your best to use clear and concise language and structure that is easy to read:
Once we have determined the structure for a figure, work to make it as polished as possible before sending to me for review so that I can provide comprehensive and helpful feedback. If you give me something unfinished, I will likely tell you things you already know. Figures should be entirely reproducible from code and should generally be saved as vector files (PDF or EPS). EPS files can be modified in Adobe Illustrator or other image-editing program. I will not review or publish figures made in Microsoft Excel.
Manuscripts from the Rife Lab will be preferentially submitted to pre-print servers and published in open access journals. You are required to send a manuscript to all authors at least two weeks before submitting it to give them an opportunity to comment. Page proofs should be reviewed carefully for mistakes (especially references).
Our lab follows the Clemson Authorship Policy. Many journals now require the assignment of CRediT roles to each author (Conceptualization; Data curation, Formal Analysis, Funding acquisition, Investigation, Methodology, Project administration, Resources, Software, Supervision, Validation, Visualization, Writing – original draft, Writing – review & editing). Since projects evolve over time and authorship inclusion and order are re-evaluated accordingly, it is good practice to assign these roles to each author of manuscripts you lead. If you feel that your contributions to another’s work merit authorship but you have not been included as an author, please discuss this with Trevor.
Existing literature provides the foundational knowledge and theoretical framework necessary for our current work and can be used to identify gaps in what has been done previously or inspire new research questions. Keeping up with published literature, allows us to build on the past without unnecessary repetition and continue to move the field forward. Papers can also be a great source of protocols, code, and data that can be used to design experiments and frame analyses. They may also cite other relevant work that you can find and read to help further understand concepts.
Manuscripts may be hidden behind a paywall, but don’t let this stop you from reading them. Clemson University libraries subscribe to many scientific journals and are often able to obtain specific articles outside of those subscriptions through Inter-Library Loan services. Google Scholar, PubMed, and ResearchGate often have alternative links to get the full text of an article or authors may have manually uploaded their full text. If all else fails, corresponding authors are nearly always willing to send a copy of their articles when direcly asked.
Before you start reading, obtain a PDF reader and citation management software. Organizing your papers as you find and read them will make it substantially easier to find them later when you need to use them as references. Clemson provides Adobe Acrobat for free to students, staff, and faculty. Zotero is a free, open-source citation manager and PDF reader that is useful for organizing, annotating, and citing papers.
When you’re organized and ready to read, start with the abstract, which provides a summary of what was done and the results and conclusions from the work. From here, your reading strategy may change depending on your goals. Typically, the figures are a good place to start. Ten simple rules for reading a scientific paper is a good resource for optimizing your time spent reading and efficiently navigating scientific papers.
All lab members are encouraged to attend at least one conference per year to present a poster or talk related to research being performed in the Rife Lab. Travel grants are often available through multiple sources including the department, university, or organizing conference and lab members are expected to apply for these opportunities to help cover travel expenses. Members of the lab regularly attend the ACS Tri-Society Meeting, Plant and Animal Genome Conference, and the National Association of Plant Breeding Annual Meeting. Lab members can attend other conferences that are topical to your research projects and align with the supporting grants. Members who are invited to conferences or other meetings with their costs covered are welcome to accept such invitations.
Anyone planning to submit an abstract for a conference, symposium, etc. must first clear this with Trevor and circulate the abstract to all authors at least one week before the submission deadline. Failure to meet this deadline will result in you not attending the event.
Scientific career progression is heavily dependent on your ability to effectively present your research. It is therefore highly encouraged that you seek opportunities to regularly present your research, whether it is at a departmental level, to other labs (within or outside of Clemson), at conferences, or to the general public. Every time you present your work, you are representing the entire lab. Practice talks will help you feel comfortable with your presentation and allow you to get direct feedback from the lab. If you are going to give a presentation, be prepared to give a practice presentation to the lab prior to your real presentation (at least one week for posters, two weeks for conference presentations, and four weeks for job talks).
Posters must be circulated to all authors at least one week before the printing deadline.
Templates for posters are available in the posters repository and final posters should try to match the overall design and style of the template.
General rules for posters: minimize text as much as possible, make figures and text large and easy to see at a distance, label your axes, and make sure different colors are easily discriminable.
Make sure to double and triple check that your dimensions match the requested size and orientation for your event (especially orientation!).
For oral presentations, watching online seminars from scientists in the field is a good way to refine your presentation style and content. Trevor is happy to share slides from some of his talks if you would like to use a similar style. As with posters, feel free to go with your own style as long as it is polished and clear. Internal practice talks should use your final slides and be near the right length to ensure feedback is as helpful as possible.
All work-related travel must adhere to the Clemson travel guidelines, the Clemson Travel Procedure, and the Clemson Travel Policy. All overnight travel requires university pre-approval through a travel request. Reimbursements for university-related travel are made entirely through Concur. Per diem follows the GSA rates and can be found here. To add per diem to your travel request, choose the “Travel Allowance” option.