Structuring a UR Experience

There are a number of techniques that can be extremely useful in becoming an effective self-directed student researcher. In this section, we will discuss several of these techniques that your research advisor and research group may employ, specifically, research proposals, research learning contracts, standard operating protocols (SOPs), group meetings, journal clubs, and reflective journaling.

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Standard Operating Protocols (SOPs)

Standard operating procedures or SOPs are written step-by-step procedures that quality control (QC), quality assurance (QA), and production units use in order to assure the accuracy and precision of the quantitative experimental results and materials that they generate and provide in support of other units such as Research and Development (R&D), manufacturing, etc. SOPs are generally used in support of experimental research whenever there is a need to document the handling of samples, the methods used in their analysis, and the quality of the results generated in the analysis of these samples. SOPs are used by the governmental agencies, private industry, and academic laboratories by scientists and engineers from all of the science, technology, engineering, and mathematical disciplines. Examples of their use include forensic analysis where they are used to establish the chain of custody of evidence and in private biotechnology industry where they are often used to validate new methods of bioanalysis. SOPs can also be extremely valuable in academic laboratories and can be employed anytime there is procedure that potentially more than one person will use in a research group. They can be written to:

  • outline sampling procedures, describe the proper procedures for the transportation of research materials;
  • standardize the methods of training for often used experimental methods and/or analytical instrumentation; and to
  • document the methods used in data handling and/or analysis.

To be effective, SOPs need to describe not only what needs to be, but who is qualified to carry it out, and under what conditions the procedure can be performed reliably.

How do you know if an SOP works? Test it. The best way is to have someone else in the lab unfamiliar with the technique try to follow the SOP to carry out the procedure. SOPs must be reviewed periodically for accuracy and completeness by other scientists who have experience doing the procedure. As such SOPs are invaluable in documenting that the experimental procedure was accomplished properly.

SOPs can be invaluable to students involved in undergraduate research in providing written guidelines detailing how to carry out new/unfamiliar methods reliably. The action of authoring an SOP can be beneficial in helping you to think through the procedures you use in a thoughtful step-by-step manner and document clearly and succinctly in writing your understanding. Thus, the SOP saves you, the author, and those using the SOP precious time and effort since it lays out exactly what must be done in order to achieve the desired results and it provides a timeless means of sharing that information with all who may need it both now and in the near future. Authoring SOPs provides undergraduate students an opportunity to document and showcase their understanding of the methods used in their research and of the quality of their written communication skills.

Example SOP

The following are the main sections you will find in most SOPs together with a brief description of the content of each suggested section. Note that not every SOP will have each of these sections. However, in general, the more information provided, the better the quality of the SOP and the more generally effective the protocol will be in the laboratory.

  1. Title – a clear, succinct title describing the purpose of the SOP and the conditions under which it can be reliably used.
  2. Date – date (including year) of authorship of the current SOP. If the SOP has been revised then a “Date of Revision” and the “Revision Number” should also be included here.
  3. Name of the Author of the SOP – self explanatory
  4. Purpose – Brief explanation of the purpose of this SOP
  5. Scope and Applicability – under what specific conditions can this protocol be used reliably; are there any known interferents or other limitations on the protocol’s effective use?
  6. Introduction – relevant background information on the system, methods, and instruments used.
  7. References - any relevant references to the peer-reviewed literature
  8. Materials and Supplies – list of any reagents including names of suppliers used in this procedure. If the suppliers are obscure sources, a list of addresses and contact information should be provided as well.
  9. Analytical Instrumentation – list of any analytical instruments including manufacturer and model numbers that have been used in this procedure.
  10. Cautions – are there any specific health and safety precautions that should be considered. For example, should gloves be worn? If so, what kind? How should spills, if they occur, be cleaned up? Are there any special procedures that should be followed in order to safely dispose of waste?
  11. Personnel Qualifications – what if anything must the user know or be able to do before being able to carry out this protocol, i.e., is any prior training required and if so what specific kind/form of training?
  12. Names of SOP Reviewers - names of those individuals who have reviewed and approved the SOP for use in the laboratory. Signatures and dates should be provided whenever possible as well.
  13. Actual Protocol – step-by-step set of instructions for accomplishing the procedure of interest reliably. If calculations are involved in analyzing the data, then an example of the calculation should be provided. Figures and tables showing laboratory apparatus, representative data, etc. can be included here.

You will find an example of an SOP here.

Example SOP

TITLE: Preparation of the Perfect Cup of Coffee by the Drip Method
Date of Preparation:


Date of Revision: N/A

Revision No.: N/A

Submitted by: Ay Dot Student

Approved by: Professor Ex

Purpose:Provide an example of a standard operating protocol or SOP that can be appreciated by undergraduate research students from all academic disciplines.

Scope and Applicability: The following protocol can be used wherever quality coffee beans, good drinking water, and a drip coffee maker are available.

Introduction: Coffee is the beverage of choice of many college students. Properly prepared the beverage provides an invigorating and revitalizing effect. One of the most frequently used methods of preparation is the drip method. In this method, water, heated to near boiling temperatures, is slowly added to finely ground coffee beans held in a filter unit. The coffee beverage is collected below the filter unit in a glass carafe. Today this procedure is frequently accomplished using a semi-automated process in an electronic coffee maker. The procedure below outlines a reliable method for preparing drip coffee using any commercially available drip coffee maker, high quality ground coffee beans, and filtered water.

References: For information on coffee beans, the standard methods of preparation of coffee, and recipes see:

Materials and Supplies: Freshly ground Starbucks® coffee (any flavor you prefer; medium grind works best with most commercial coffee makers), commercial 4-c drip coffee maker including filter (gold mesh preferred but high quality paper filter may be used), good quality drinking water (Polar Springs®, Brita®-filtered, or similar quality source recommended), coffee cup, and additives (as desired: sugar or sugar alterative, cream or milk).

Cautions: Hot coffee can scald and burn. Water is an electrical conductor. If spills occur during the brewing process, wait until the brewing process is complete, turn of the electricity, and disconnect the unit from the electricity before attempting to clean up any spills. Accidental spills may be cleaned up with a kitchen sponge and dish washing detergent such as Dawn®, Dove®, or Ajax®. Used coffee grounds can be disposed of in the regular trash. Be sure to carefully read the directions that accompanied your coffee maker unit before attempting to use it. In particular, it is important to find out if your unit has (1) a pause feature that will allow you to remove the carafe while the coffee is brewing; and (2) an auto-off feature that turns off the heater unit located beneath the carafe at a set time after the coffee has been brewed.

Personnel Qualifications: No special knowledge or training is required to make coffee. However, due to the potential risk of burns, it is recommended that anyone performing this procedure who is less than ten years old be actively supervised by an adult.


1. Make sure that the coffee maker is off. Locate water reservoir unit on coffee maker and carefully add 4-cups of clean drinking water to the reservoir. Note that the outside or inside of most quality coffee makers’ water reservoir units are marked for the user’s convenience.

2. Locate the coffee filter assembly on the coffee unit. If you are preparing the standard 4-c carafe of coffee, carefully measure one coffee measure of ground coffee into your units coffee filter assembly. Note that one standard coffee measure is equivalent to 1/8-c of coffee. Close the coffee filter assembly.

3. Plug in the coffee maker and turn the unit on. Wait until the carafe located beneath the coffee filter unit is filled with coffee. Note that some units may have a “pause” feature that will allow you to temporarily remove the carafe and pour a cup of coffee while the unit is working. If you are unfamiliar with your unit, be sure to wait until the unit is done filtering before attempting to remove the carafe.

4. If coffee spills beneath the base of the carafe unit, be sure to turn off the unit and disconnect the electricity before attempting to clean up the spill.

5. Pour yourself a cup of coffee. Most coffee units will keep the carafe warm for a set period of time before turning off automatically. Some however, do not turn off automatically. Be sure to read your coffee maker’s instructions beforehand. If in doubt, be sure to turn off the electricity to your unit after the brewing process is complete.

Group Meetings

A standard element of the learning environment in most research groups at graduate research institutions is the so-called "group meeting." Group meetings are usually meetings of the research group, i.e., the research advisor or advisors, in the case of interdisciplinary research teams, and all of the members of their research groups including post doctoral students, graduate students, undergraduate students and technicians. The purpose of these meetings is usually to discuss research progress, problems, and new ideas. Some advisors however use group meetings as an opportunity to critically discuss articles from the current peer-reviewed literature (same thing as a Journal Club).

Group meetings are typically fairly informal but this depends on the personality of the research advisor. Some advisors like their students to give formal research presentations (PowerPoint-style) using laptops and projectors. Others prefer that their students be able to discuss their recent results in the form of so-called "chalk talks." These are informal presentations made on the fly without the aid of handouts, slides, transparencies or other pre-prepared visual aids. Group meetings are often held weekly. These meetings have no set length as a rule and may be as short as an hour or as long as a day depending on the research advisor.

If you lab doesn't have group meetings, consider suggesting that the group start having regular meetings. If you offer to make the first group meeting presentation, your advisor is even more likely to take you up on your suggestion. So consider making the offer if you are serious about doing this.

Rules of Etiquette for Group Meetings

  • Attend all group meetings. If you are unable to attend, it is important to notify your research advisor well in advance of the meeting and to provide appropriate justification for your absence.
  • Show up on time, prepared and ready to participate. Bring a pen/pencil and a notebook in which to take notes.
  • Be sure that you turn your cell phone off before entering the meeting room. If you forget to turn it off and your cell phone rings, attend to it immediately (don't let the ringer keep ringing) and take your conversation outside the meeting room.
  • If you are late, apologize and settle in as quietly as possible so you don't disturb the flow of the meeting already in progress.
  • Participate actively in group meetings. Ask questions. Volunteer to help out if requests are made for assistance with group related activities.
  • Inquire in advance of the meeting concerning whether or not it is acceptable to eat and/or drink at group meetings. If food and drink are permitted, be sure to clean up after yourself when you are finished.

Journal Clubs

In graduate school, it is a common practice for groups of students with a common interest get together to read and discuss articles in a particular field or subject. These meetings are frequently identified as "journal clubs." Reading and discussing articles with others who share your interests and background will really help you get the most out of the articles that you read and the community aspect will also help keep you motivated and at the same time provide a useful degree of personal accountability. If you are working at a graduate research or comprehensive university there may already be some active journal clubs in your department. If not, there are any ways to organize and run journal clubs. No matter how you choose to do it, you will find it works best when:

  • The group meets regularly in the same location at the same time - a weekly frequency is probably best as this gives everyone some breathing room;
  • Responsibility for leading the discussion of articles is rotated among all of the regular participants;
  • Articles selected for reading and discussion are of interest to the majority of the group; and
  • Everyone participates actively in the discussion of the articles.

Useful Questions for Guiding Journal Club Discussion

Here are some useful general questions you may find it to consider when reading and discussing articles from the current peer-reviewed technical literature in your Journal Club:

  • What type of article is this?
  • What is your evaluation of the presentation of the science in this paper? Possible areas for consideration include:
  • What if any personal biases are you bringing to this evaluation?
  • What, if anything, do you know about the authors of this paper? What is their field of expertise? What other papers have they published in this area recently? How is that work related to the present paper?
  • What is the quality of this journal?
  • Is the paper well written? Grammar? Style? Clarity of the presentation? Is the language vague or unclear?
  • What is your evaluation of the quality of the work described in this paper?
  • What is the quality of the materials, methods, and instrumentation used to carry out this study? How were data analyzed? What is the quality of the interpretation of the data?
  • What are the strengths and weaknesses of the chosen experimental design?
  • For quantitative work, what if anything has been done to evaluate the validity and reliability of the results?
  • Are there any errors that the authors may have missed? What do you believe may be the impact of these errors on the authors' data, interpretations, and/or conclusions?
  • What is the overall significance of this work to your field of study?

Reflective Journaling

Doing research is very different from carrying out a traditional course-related lab experiment. The solutions to research problems are not normally known at the outset and often the outcomes are very different from those envisioned at the outset. Each research problem is unique. In addition, each researcher brings with him/herself his own unique set of skills, understanding, and experience with which they will approach their research. Thus, it is essential to be able to effectively leverage one's professional skills and experience in an autonomous and competent manner in the real-world workplace.

Reflective journaling can be an extremely useful tool in this regard. If you are not familiar with this technique, you are not alone. Not often used in the science and engineering fields but a standard practice in clinical training and the field of education, reflective journaling is regarded as an extremely useful and powerful technique for affecting self-discovery and personal and professional growth. The act of journaling involves the regular practice of recording activities and/or situations on paper or electronically with the goal of reflecting on those experiences in order to learn from them and grow personally and professionally.

Journaling is useful in providing insight into self-awareness - what you do (behaviors), why you do it (values, assumptions, aspirations) how you feel (emotions), and how you think. Journaling can expose contradictions, misconceptions, and conflict. In short, it helps you turn every incident into a new potential learning experience.

It is important to understand though that journaling isn't merely the act of chronicling one's experiences. Writing about one's experiences can be useful as it helps to make explicit knowledge that one may have learned and practiced implicitly for better or worse. It also helps to provide perspective and structure to daily events that sometimes appear chaotic and random. However, educational research suggests that active reflection is needed if true transformational learning is to be realized.

In this section we will discuss:

Paper-Based or Electronic?

Journals can be either paper-based or electronic. You can keep a journal on sheets of paper which you can organize in a three-ring binder or write in any small bound notebook. Electronic journals can be maintained on a computer, laptop, or personal digital assistant (PDA). There are a growing number of software packages available for electronic journaling such as Life Journal but any word processing program like Microsoft Word, WordPerfect or even Notepad will serve as well, too.

Paper journals have the advantage of portability and availability though with the increasing multi-functionality of PDA's and similar devices, these are no longer clear advantages. Electronic journals have the advantage of superior readability and indexing and cross indexing functionality. However, electronic journals may be irretrievably lost if accidentally deleted or if the electronic device catastrophically fails. Electronic journals also afford the user confidentiality as these can be password protected in case the electronic device is lost.

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General Guidelines for Reflective Journaling

Journals work best when entries are:

  • Regular made on a consistent periodic schedule;
  • Reflective not merely descriptive chronicles of events but critical assessments/analysis of the situation and/or behavior; and
  • Transformational meaning that specific, doable strategies for change are identified and subsequently implemented.

Entries need not be lengthy to be meaningful.

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Examples of Useful Questions for Reflection

Depending on your goals and individual nature, your journal can be either more or less structured in format and style. One important thing that is known about journaling is that for it to be effective the journal must be more than merely a written record. A set of guiding questions can be useful in facilitating critical reflection if the questions motivate you to reflect. For this reason the following questions are offered as useful starting points in facilitating meaningful reflection.

  • Briefly describe a situation that occurred in lab this week that affected you as an individual or your team (if relevant) as a whole.
  • Why are you describing this incident - did you experience challenges in meeting it? Did you exhibit strengths? Did you learn something?
  • Is there an overarching issue or problem here? What is the potential value here?
  • What were you feeling at the time of the incident?
  • What were you thinking at the time of the incident? Did you have any preconceived ideas? New insights?
  • What was good or bad about the situation?
  • (How) Has this experience challenged your assumptions, prejudices, or biases?
  • What specific possible solutions have you been able to identify to the problem?
  • (How) will this experience alter your future behavior, attitudes, or career?

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Research Learning Contracts

One pedagogical technique that you and your advisor can use to structure and assess your undergraduate research learning experience is a research learning contract. The research learning contract has long been used in adult education where the learning experiences are often highly self-directed as in the undergraduate research experience. Research learning contracts provide form and structure to what is a relatively unstructured learning environment (the research laboratory) while at the same time ensuring maximal flexibility which ultimately puts you, the student, in control of your own learning. Research learning contracts do this by allowing you to define the learning objectives, learning activities, your rate of progress, and the method(s) of assessment that will be used to evaluate your eventual success or failure which helps ensure that you will be successful.

The research learning contract is a contract in that it is a formal written agreement between two parties, you, the student, and your research mentor, defining what is to be learned, how it will be learned, and the terms whereby learning will be demonstrated/assessed. However, it defines the process of learning rather than the content. So, it is not a syllabus. In this way, it allows each student learner to structure his/her learning environment to meet his/her unique needs. It is also unlike a formal contract in that research learning contracts are intended to be periodically revisited and renegotiated in order to ensure that all parties are deriving maximal benefit from the learning arrangement defined by the contract. Research learning contracts are also not research proposals. They emphasize process rather than content and should contain the minimum amount of information needed in order to define the process as their purpose is to provide a modicum of structure while at the same time providing maximal flexibility. In this section we will offer specific information and advice on how to create and use your own research learning contract in support of your undergraduate research experience.

In this section, we will discuss:

Content And Form

There is no set content or specific required form for a research learning contract. However, research learning contracts usually contain the following types of information:

  • Brief descriptive project title
  • Names and contact information (office address, cell phone, email) for the faculty advisor, student, and whomever will be providing daily supervision, if the faculty advisor will not be serving in this role
  • Projected start and end dates for the project
  • Specification of student’s role on the project – volunteer, salaried, for academic credit, etc.
  • Goal(s) of the project – the long term purpose of the project
  • Objective(s) of the project – these should be short term, bite-size achievable aims with realistic target dates for their accomplishment
  • Identification of any significant safety considerations
  • List of any needed resources (bibliographic, training, materials, equipment and/or instrumentation) – this identifies the commitment and responsibilities to be provided by the faculty research mentor; and
  • Anticipated Outcome(s) of Project such as term paper, oral presentation, thesis, etc.

It is totally up to you and your advisor what you choose to include or exclude from your research learning contract.

From an instructor’s vantage point, research learning contracts are attractive because they facilitate student ownership of and therefore commitment to the project and the research plan by allowing the student learner to define the learning objectives, learning activities, and assessment methods. So, it makes explicit for both the student and the research mentor the project’s objectives and process and ensures mutual agreement by both parties.

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Examples of Research Learning Contracts

The following are two examples of research learning contract for undergraduate research experiences in the field of chemistry.

Research Learning Contract 1

[Student Name]
[Faculty Mentor’s Name]

Objective: The objective of my research will be to obtain spectroscopic evidence through resonance Raman of the effect that potassium chloride has on the catalytic activity of horseradish peroxidase in different organic solvents.

Research Purpose: …The resonance Raman study will help to elucidate the mechanism of salt-induced enzyme activation in non-aqueous media, specifically, the effect of potassium chloride on horseradish peroxidase in acetone and acetonitrile.

Methods: Horseradish peroxidase will be co-lyophilized with varying concentrations of potassium chloride, dissolved in aqueous potassium phosphate buffer or suspended in acetone and acetonitrile, followed by spectroscopic study of the sample by Raman.

Personal Goals:

  • To increase my understanding and proficiency in Raman
  • To learn freeze drying while increasing my experience with UV-vis
  • To learn to keep a reliable record of my work in the lab while increasing my confidence working in a laboratory setting
  • To obtain results that warrant publication, whether as a paper or poster with the option of presenting the paper or publication at a conference
  • To be a sponge and absorb everything or as much as is humanly possible in an academic quarter

Lab-Time: I will devote 4 hours on Tuesday and Thursday throughout the spring quarter for a minimum of eight hours each week. If needed and if my schedule allows it, I will increase the lab time.


Research Learning Contract 2

To: [Faculty Advisor Name]
From: [Student Name]
Subject: Work Contract and Tentative Schedule

UV-vis spectroscopy revealed a correlation between the electronic structure of polypyrrole and solvent polarity. I would like to pursue additional characterization of supercritical carbon dioxide synthesized polypyrrole films by examining their structure with UV-vis, Raman, and FTIR methods during my work-study this quarter. My objectives are:

  • To learn and understand Raman and develop my experimental expertise in this technique
  • To learn and understand FTIR and develop my experimental expertise in this technique
  • To expand my understanding of UV-vis spectroscopy
  • To characterize aqueous (sulfuric acid), non-aqueous (acetonitrile), and supercritical carbon dioxide synthesized polypyrrole films with the above methods
  • To analyze my data and compare the results to my previous UV-vis findings
Time Week Planned Tasks
8 hours 1 Synthesize polypyrrole films*
8 hours 2 UV-vis and Raman characterization of polypyrrole films
8 hours 3 Continue Raman and prepare summary of mechanism, instrumentation and information obtained from Raman technique
8 hours 4 FTIR characterization of polypyrrole films
8 hours 5 Continue FTIR and prepare summary of mechanism, instrumentation and information obtained from FTIR technique
8 hours 6 Analyze all data and summarize results

*Note: Synthesis may take longer or I may need to make more polypyrrole films throughout the quarter. I will need to synthesize at least two films (preferably 3) with each method in order to ensure repeatability.

[Faculty Mentor]

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Do's and Don'ts

Research learning contracts are most effective when:

  • Student authored, i.e., written in the student’s own words. Don’t let your research mentor even if they are well meaning write the learning contract. If there is some idea that you can’t seem to express in writing. Likely this means that you don’t really understand it. If there is something that you don’t understand about the project, explain that to your advisor and ask him/her to explain that concept or aspect again so that you understand and can write about it yourself using your own words.
  • Short rather than lengthy. They should be no longer than two pages in length and contain a minimum of information in order to be maximally effective as their purpose is to provide a modicum of structure while at the same time providing maximal flexibility.
  • Created at the outset of an undergraduate research experience. This ensures that you and your advisor are in agreement from the outset concerning the nature of the problem you will investigate, the methods you will use, the time you will commit, and the methods that will be used to evaluate your success; and when
  • Signed by both the faculty mentor and student during the first or second week of the undergraduate research experience. Signatures are evidence of your and your advisor’s buy-in to the project, the specifics outlined, and your new working relationship.

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First Steps

If this is your first exposure to the idea of a research learning contract, you may find it useful to use a template in constructing your own. Simply complete each section here and click on the “Submit” button at the bottom of the form to generate your own research learning contract. Alternatively you might wish to examine some of the learning contract forms used at other institutions. The following are examples of several good learning contracts:

  • North Carolina Wesleyan College (Criminal Justice internships)
  • Macalester College


Coming soon.

Learning Contract Template

Coming soon.

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