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Finally, X. also agreed with V.’s assessment of the difficulty consolidating information about experiment protocols. X. said that the current method of combining handwritten notes is grossly inefficient and error-prone. Like V., X. would like to have some interface which provides an easy way to take shareable e-notes about particular experiment protocols with step-by-step instructions and comments from different team members about their experiences implementing that protocol.
4. J.
J. is a postdoc in a biology lab at MIT. We spoke with him about issues he has with finding a usable protocol for experiments in the lab, as well as issues with communicating with his collaborators in computational fields.
When trying to find a protocol for a particular experiment, he finds that published papers do not usually include all the details required for running a particular experiment under certain conditions. For example, Nature Protocols has some standardized protocols available, but with none of the details that biologists typically require to actually run the experiment under specific conditions. He said that he often has to spend a lot of time asking advice from many different people in his lab or other labs who have experience with the particular experiment or conditions he is investigating. He thinks it would be helpful if there were one centralized version of each important protocol for the whole lab to avoid this process, but he noted that most labs would not want to share this protocol with other labs except for their collaborators until they published a paper about it.
J. also spoke about issues he has with collaborating with computer scientists or computational biologists. One common scenario is that he wants to perform some analysis on his data, so he needs the collaborator to write some computer code to run the analysis. Often it is more efficient for the collaborator to give the completed code to J. than for J. to make many requests for different datasets and different parameters, but then J. has to figure out how to run the code on the command line. Although the collaborator might give good instructions and documentation, J. is not used to using a Unix terminal and finds it intimidating and confusing.
We were interested in J.’s difficulty with using a command-line interface, so we asked him to run some code for us, such as a tool commonly used for RNA transcript assembly called Cufflinks. The first issue he ran across was that he couldn’t remember his password to ssh to the server, since he rarely needs to perform this task. Once he finally connected, he said that he didn’t have time to show us a realistic example, since before running any code (such as Cufflinks), he would need to spend a lot of time reading about the program. Instead, we asked him to perform some simple tasks, such as finding the number of lines in a file using the command line. He had the following difficulties:
- He didn’t know off the top of his head how to find the number of lines in a file, so he googled for “unix line numbers” and found some entries about the command “nl”
- Once he realized that nl did not do what he wanted, he searched more carefully and found the command “wc --l”, but misread the l as a 1.
- Eventually he tried just running “wc”, which outputs three unlabeled numbers. He guessed that the smallest of the three numbers was the number of lines, but was not sure.
Lessons learned
- Feels that published protocols do not contain all the necessary details
- Would like a way to easily share protocols and related notes within the lab as well as with collaborators
- Finds common tasks on a Unix terminal very difficult due to a lack of learnability of commands and command-line options
- Typically resorts to outside sources such as Google for documentation since it is easier to find usage examples
- Confusions such as “-l” with “-1” can occur, so they must be avoided.