# General Information for Lab Members

[EcoEvoDevoLab](https://hackmd.io/@EcoEvoDevoLab/AngeliniLab)

Updated 9 September 2023


> Angelini lab alumni, Abbe Labella '10 (AU) and Ariel Aspiras '12 (MS, AU).

The lab is yours. It exists to allow you to do research that provides you experience in the practice of science, exposure to details of biological knowledge, and furthers humanity's understanding of development, genetics and evolution. Importantly, these goals should be met in a way that is ethical, safe and fun!

- As a member of the lab, you are free to be there at any time. Conducting experiments should always take priority, but as long as space allows, you are welcome to use the lab to study or just hang around while a friend is working.
- If you're in the lab outside regular business hours, don't work alone. Bring a friend. You should also call campus security to let them know you're there.
- You are welcome to have guests in the lab, as long as they follow basic lab safety rules and don't disrupt the work of any other students.

## Your role in the lab

### Independent study

The typical expectation of an independent study is of 3-4 hours per credit per week. So, for a 3-credit independent study (the most common), it would be about 10 hours / week. That time is meant to be flexible, and it can shift over a semester. It should average to that number. You should dedicate specific blocks of time each week when you will routinely be in the lab working on the project. Independent studies for fewer than 3 credits can be problematic, especially if you haven't already worked in the lab, since procedures and experiments require regular attention and momentum. Similarly, it's not a good idea to cram an independent study into an already full course schedule, since with regular classes there's always deadlines to meet. In a busy semester independent lab work often gets pushed aside. That's not good for the successful completion of the project.

For an independent study of any credit amount, I usually define a successful semester as one where you're in lab making an earnest effort, keeping good notes, and asking for help when necessary. A write-up of the semester's research in the format of a journal article is usually the final requirement.

The grade is based on the quality of all of the above. Keep in mind that 4 credits of independent study can be counted towards the biology major. However, independent studies do not count towards the number of lab courses you must complete for the biology major requirement. Remember JanPlan independent studies are possible too!

An independent study must be added before the Add Deadline (typically one week into a semester). Do so in your My Colby web portal. Choose a title that will appear on your transcript. You should also draft a project description, which I'll edit if necessary.

### Research assistantships (RA)

If you qualify for on-campus employment, you can be paid for work in the lab during the academic year. RA students can (and typically should) be intellectually engaged in the lab work. RA positions are limited, and while they are advertised on WorkDay, these are typically not open searches. Support for summer RAs can also be requested from the Dean's Office in January of each year. If you'd like to work in the lab over the summer, let Dr.A. know before the New Year!

### Volunteering

Volunteers are under no obligation and can drop their association with the lab at any time. However, students don't get anything official from this experience. This may be a good option for a motivated student who already knows what they're doing, or can learn from a friend in the lab.

### Honors thesis projects

Seniors majoring in Biology or Computational Biology can conduct a two-semester research-based thesis project to graduate with honors. The honors project is a substantial commitment. Unlike an independent study, a thesis project requires that experiments "work" in the sense that you must successfully gather data that tell a story. For this reason, I will only sponsor honors students who've worked in the lab previously and demonstrated research productivity. Projects need not be closely related to past work, but should fall under the lab's larger research orientation. The thesis will also require a significant writing component in which you review the background literature.

An honors proposal must be submitted to the biology department by the end of your junior year. More details and critical deadlines are online http://www.colby.edu/bio/resources/honors-program/.

### What to do if you discover you really don't like being in the lab?

I want students to tackle projects with enthusiasm and intellectual curiosity. If the lab doesn't seem exciting after a few weeks, let me know. Projects are always most successful when folks are committed to them. But it's not for everyone. No hard feelings! Nothing in the lab is so important that you should be miserable, and there are always ways out of an independent study or honors project.

### Letters of recommendation

I am willing to write letters of support for students I've known or worked with in any capacity. My comments will summarize your work in lab (or class) and reflect my honest opinion of your skills, dedication and maturity. If I think that honesty would prevent me from writing you a letter that is supportive, I will gently ask whether another faculty member might be better suited to writing for you. There may also be rare circumstances when other demands simply make it impossible for me to meet letter deadlines, in which case I may need to decline.

## Responsible Conduct of Research

The College also requires research students working in any capacity outside of a regular course to undergo online training in research ethics. This goes beyond lab safety to include workplace conduct and professional responsibility. Here are some important considerations.

- Publication is a goal for all projects, and the criteria for authorship may vary depending on the project. Typically, to earn authorship you must do more than one of the following:
- Make a significant intellectual contribution to the project, such as experimental design or data analysis
- Make a significant contribution of labor towards the project, such as multiple semesters of lab work
- Make a significant contribution in writing, such as drafting a manuscript section or assembling a figure

Since compiling data for a manuscript may take many years, your data might not be published during your time at Colby. So, you may be contacted after graduation. In some cases, data may never find their way into a publication. All authors must approve a manuscript before it is submitted for review and again before final publication.
- While our lab does not work on human subjects or vertebrate animals, our research animals are living creatures worthy of humane treatment. Their use in the lab serves your education and advances human understanding of biology.
- Humane ways to euthanize insects include placing them in the freezer overnight, or immersing them in liquid nitrogen. Bugs can also be anaesthetized using CO~2~, and immersed in 70-100% ethanol.
- Bugs should not be allowed to starve or die of dehydration or disease.
- Once insects are in the lab, they cannot be released into the wild under any circumstances. Release would jeopardize the health of native animals and ecosystems.

## Lab Safety

As a participant in lab research, you will be expected to know basic lab safety rules.
- Questions about how to do something safely? Ask Dr.A. (x5734) or a technician.
- Follow good housekeeping practices!
- Clean up after yourself.
- Wash glassware and instrument after you have used them.
- Keep work areas, aisles and exits uncluttered.
- Don't monopolize tube racks. Keep samples from your project in labeled freezer boxes.
- Don't leave the CO~2~ on.
- Do not eat, drink, smoke or apply cosmetics or contact lenses in the laboratory.
- Do not store food or drink in the laboratory, or use laboratory equipment for cooking, baking, or spa treatments.
- Wash hands after handling bacteria, insects or chemicals, and before leaving the lab.
- Be careful not to contaminate personal electronic devices, including phones, with biological materials or chemicals that may be on your hands or gloves.
- Remove any protective gear before leaving the laboratory; this includes gloves and lab coats. Beware of contamination of clothing or doorknobs.
- Know the potential hazards of the materials and equipment with which you will work. Just search for "MSDS" and the chemical name online.
- Wear personal protective clothing, such as a lab coat or safety goggles, when experimental conditions dictate.
- Wear a full UV face shield when working over a UV light box. No tanning.
- Wear clothes that protect against potential chemical spills. This means avoiding shorts or short skirts, open-toed shoes, or flip-flops.
- Confine long hair when in the laboratory.
- Remove or secure ties or other articles of clothing or jewelry that might tangle in equipment.
- Know the location of exits from the lab and building, in case of an emergency.
- In the event of an accident or safety concern:
- In case of a serious fire or other life-threatening emergency, call 5911. A phone is right of the lab sink.
- For other situations, contact Dr. Angelini (x5734) or another faculty member.
- A chemical safety shower is in the hall outside Arey 301.
- An eyewash is left of the Arey 301 sink.
- A fire extinguisher is right of the sink.
- Do not work in the lab alone, unless someone knows you're there and when you should return. You can always notify Campus Security of your presence (x5530).

### Compressed Gas Cylinders

Compressed gas cylinders are potentially dangerous even if they contain nonflammable gas. In our lab we usually deal with CO~2~, which is not flammable. However, if a compressed tank is damaged, the escaping gas can rocket the cylinder through a wall.


- To operate a gas cylinder, just open the main valve (counter-clockwise). Normally, don't adjust the other valves.
- Turn the gas off when you're done! -- If the valve is left open the cylinder will run empty in a matter of hours. We only get deliveries of refills once per week.
- If a cylinder is empty, ask a technician or faculty member to switch to a spare.
- If you do need to remove the regulator, use a wrench (there's one in the insectary or under the sink in 301) to loosen the connection of the regulator to the cylinder's stem. Be careful to keep the white Teflon washer with the regulator.
- Gas cylinders should always be capped if they are not hooked up to a regulator.
- Cylinders should only be moved using a cylinder cart. One is available below the stairs in the Arey basement.
- Cylinders should be shackled to a wall or bench , except while being moved. Even empty cylinders should not be left freestanding.
- If you start a new cylinder or empty one in use, then flip the ring that indicates "empty/full" status.


## How to Keep a Lab Notebook

A lab notebook is the way scientists keep track of their work. It may sometime seem tedious or even unnecessary, but it is an important part of laboratory work. In the biotech industry, a lab notebook is a legal document, on which million-dollar patent claims may depend. The notebook should be complete enough that you or another student could refer back to it in a few years and repeat your experiments.
- Handwriting in your lab notebook must be legible.
- Use pen; not pencil.
- Date each entry. Notebooks must be organized.
- Use a section heading for each entry. Make it descriptive.
- Use complete sentences, tables and graphs where appropriate.
- Errors should be crossed through with a single line, not erased or obliterated.
- Long protocols may be pasted in, but your notebook should not simply be a collection of paper.
- If you use the protocol from a kit without modification, you can simply refer to it.
- Any deviations from the protocol as provided must be noted and explained. If there is room in the protocol for variation (e.g. “Add 5-10 ml”), record exactly what you did. This includes changes both intentional and accidental.
- Everything you do in the lab should be recorded in your lab notebooks, including notes, drawings, data, ideas and speculations. Everything from your initial strategy through planning, execution and interpretation should be in your notebook.
- Keep in mind that reports, presentations and publications will be prepared from the notebook. You should have much more information recorded in your notebook than you can or should put into a journal article.
- The first two pages of the notebook must be reserved for a table of contents. You should refer to pages by page number and entry date.
- Include raw data and then any calculations made from them. (For example, ocular micrometer units, followed by the conversion to metric distance.)
- Not every mathematical calculation needs to go into your notes, but you should show sample calculations with units at least once.