User Tools

Site Tools


Lab Policies

The lab is a fairly relaxed place, usually stocked with grungy graduate students working odd hours. The relaxed atmosphere helps encourage scientific creativity and collegiality. There are, however, some basic guidelines for conduct.

Scientific Conduct

Please review this description of scientific misconduct. A breach of proper scientific conduct is the most grave offense that you can commit in the lab. We document and report our experiments in such a way that there can never be any question about how we obtained our results.

Here are some thoughts to help keep you on the straight-and-narrow:

  • We are trying to discover new things. It's fine to get the “wrong” result.
  • Mistakes happen. If you find you did something wrong in an experiment that leads you to question the data, let me know. We can fix the problem and try the experiment again.
  • Your conscience will haunt you if you analyze and re-analyze data trying to obtain the “right” result. If a result is p=0.06, that's OK.
  • There is usually one right way to analyze data to address the initial hypothesis. We should design that analysis based upon pilot studies. If, after doing that analysis, we find something unexpected we can do post-hoc testing and then try to replicate it with some new data.

We are increasingly making use of Pre-registration and other tools of the Open Science initiative. As a new and younger member of the lab, you can make a big contribution by helping evolve the culture of work towards these developing standards.


There is a tension in science between secrecy and openness. For our published findings, we want to be open, and provide all the details necessary for others to have confidence in our results and to be able to replicate them. For work that we have not yet reported, we want to keep our methods and results private. The privacy gives us time to check our results and decreases the chances of clever ideas being scooped! The lab wiki is divided into public and private domains for this purpose.

Record Keeping

The primary action that distinguishes good science from bad is proper documentation. I am extremely picky about the quality and quantity of documentation of our work. There are three primary tools that we use to document everything that we do:

  1. Software - Whenever possible, use an automated, scripted process to do a task. A script is inherently a documentation of the actions you took to produce a stimulus or analyze some data. Because CPU cycles are cheap compared to the cost of our time and labor, it is almost always preferable to tweak a script and re-process the data from scratch rather than make some adjustment to the data by hand. The principle is that you should at all times be able to re-create the current state of your data and analyses using only the raw-data DVD and a set of scripts. An important corollary is that any change made to the data or an analysis “by hand” must be documented on an appropriate wiki page.
  2. Wiki - Each member of the lab maintains a carefully documented wiki-page notebook. A notebook helps organize your thoughts and allows you to re-trace your steps should something unexpected occur. Additionally, the notebook is used in regular meetings with me to review progress and plan next steps. The notebook contains dated sections, in which you describe what you are working on and add any images to show stimuli or results. Some policies regarding your notebook include:
    • If it's important enough to jot it down on a piece of paper so you can remember it later, it is important enough to be in your notebook. There should be no other place where notes relevant to lab work are stored.
    • Always edit under your own account, and be sure to log-out when you are done.
    • Never edit the entries from prior days! If you find you have something incorrect in your notebook, make a correction on a new day and provide a link back to the preserved, wrong information.
  3. DropBox - We maintain a shared lab DropBox with permissions and sharing set to automatically store data in write protected directories and subject information in password protected files. More flexible directories are available for you to store the results of analyses and for other project files. A critical responsibility that you have is to ensure that every file that you have on your computer that is related to laboratory business be stored in the DropBox.

DropBox Files and Privacy

We suggest that you maintain a separate PERSONAL and WORK DropBox account. Each will be linked to a different email address. The WORK DropBox account will be linked to your UPenn email address, and is a DropBox for Business account.

The documents that you store in your PERSONAL DropBox cannot be accessed by any member or administrator of the laboratory team ever (unless you explicitly share these files).

For documents that are stored in the WORK DropBox, there is privacy in only a limited sense. Basically, everything that goes in the WORK dropbox (even if not explicitly shared) is stored forever (even if deleted from your account). Additionally, while no one else on the team can access unshared WORK files now, they will revert to be accessible (and thus readable) by the lab administrators at the time you leave the lab. Therefore, you should only store work-related documents in the WORK DropBox.

Work Hours

No one punches a clock in the lab and I don't monitor your total hours sitting at a desk. Productivity matters far more than time sitting in a particular chair. That said, it is important to be present in the lab to interact with colleagues. Grad students tend to operate on an 11 AM to 7 PM schedule. If you would like to speak with me, I tend to be in the office between 9 AM and 5 PM.

Dress Code

The laboratory is an academic environment and has relaxed, but not non-existent, dress standards. Expectations for dress are as follows:

  1. "Smart casual" is the usual standard of dress, particularly if you are attending a meeting outside of the lab. Jeans are fine, but they shouldn't be too distressed. Dress is further relaxed around the lab in the summertime, when shorts are acceptable. If knowing what to wear is a challenging topic, you may find some inspiration in these photos of what folks and other folks working at startup companies wear. Please attend to basic matters of hygiene when coming into work.
  2. When meeting with participants, a more formal standard of dress is expected. This is particularly true when working with clinical populations; please wear a tie if outfit-appr must wear a tie. Jeans are not acceptable.

Authorship and Affiliation

The main reward of research work is your name on a paper. Figuring out who goes on the author list of a paper and in what order can be a tricky business. Here are some thoughts:

  • Initiate discussions regarding authorship. Let's have these conversations early and often in the development of the ideas behind a project.
  • Generally, I will go in the last author position for work from my lab. I will almost always be the communicating author; one exception being when a post-doc is developing their own area of study just prior to leaving the lab.
  • My standard is that an author should have made an intellectual contribution and be able to give a 5-10 minute talk on the general idea of the paper and their particular contribution. Different authors might emphasize different aspects, but they should have some idea of the scientific purpose and content of the work.
  • If you have developed a new method for the laboratory, you can generally expect to be an author on the first paper that uses that method, but not on subsequent papers.

A related topic is author affiliation. It is quite common for students to conduct work in the laboratory, and then move to another position or return to their home institution by the time the manuscript is submitted. Author affiliation is determined not by where you are now but by the location at which the majority of research was conducted. Here is the policy at Nature:

The primary affiliation for each author should be the institution where the majority of their work was done.Nature submission policy

The guideline here is to ask which institution is responsible for overseeing the responsible use of funds, ensuring the safety of subjects, and being ultimately responsible for certifying the conduct of the researchers.

Therefore, unless you are a collaborator that is based at another institution at the time the work was conducted, the institutional affiliation for work conducted in my laboratory will be the University of Pennsylvania. The one exception is if you are a late-stage post-doc, and submitting the work as communicating author. It is then appropriate for you to list your current address for communication.

Letters of Recommendation

I follow Brian Wandell's policy:

If you would like a letter of recommendation, first ask me: “Can you write me a very positive letter?” I will reply honestly.

If you don’t ask, I may write a letter that (a) indicates I don’t know you very well or (b) has a very neutral tone. I will refuse to write a negative letter. I will only write confidential letters.


It seems that many (perhaps a majority) of published studies in medicine and psychology are false and not reproducible. These two articles provide an excellent lay-person introduction to the extent and statistical basis of the problem:

The Retraction Watch blog describes the circumstances surrounding retracted papers.

We are not immune to these biases. It thus pays to be skeptical regarding both your own studies and those of others. When you think about the claims you would like to make about your data, consider what Richard Feynman would have to say.

I have the advantage, of having found out how hard it is to get to really know something…I know what it means to know something…I see how they get their information, and I can't believe that they know it.Richard Feynman on the claims of “social scientists”

Also, be aware that the public part of a scientific career is a record of success, but the actual path is littered with failure. Try not to be discouraged by the inevitable rejections, setbacks, and negative results.

1) Irony alert
/home/aguirreg/html/wiki/data/pages/public/lab_policies.txt · Last modified: 2016/07/05 14:56 by aguirreg