Do you ever get frustrated writing a scientific manuscript in Microsoft Word? Maybe you’ve forgotten to add the entire source code since there isn’t a specific place to input it, or you can’t remember where you embedded that image from. Not having a way to log data or record the exact steps of your experiment can lead to science that is unreproducible.
Taking a cue from his own frustrations, John Kitchin, chemical engineering professor at Carnegie Mellon University, created SCIMAX, an open-source software specifically designed for the purpose of writing scientific reports.
“In a nutshell, I saw my needs as needs in the industry,” Kitchin told Laboratory Equipment. “I created SCIMAX to meet my needs.”
SCIMAX combines the text narration function of Word with everything else that one might need when writing a research paper. The data, the code, the bibliography—there’s a place in the program for everything, already perfectly formatted and ready for input. This is key, because doing these things in other programs can lead to serious problems.
In some cases, experts may not be able to recreate an experience because insufficient information is available. For example, the exact temperatures, or sequence of reagent additions may not be reported, or the full details of how raw data was collected and analyzed is not available in a paper. Perhaps the source code used in a simulation is not listed, so it is not clear how the physics it is simulating was approximated. SCIMAX makes all of this a moot point with templates designed for scientific reporting and built-in features to ensure all data is incorporated.
Kitchin says one of the ways SCIMAX is especially helpful is citing scientific literature.
“A typical paper may have 30 to 80 citations in it, and one should check each one,” Kitchin said. “With existing tools, I found that either impossible, or very tedious. With SCIMAX, I can mouse over a citation while reading the paper to see a tooltip of the citation to see what it refers to. If I don't recognize it, clicking on the citation allows me to open the corresponding PDF or web page, as well as search for related articles if I need to add additional references.”
SCIMAX is also a better fit for scientific images than most text processors. In Word, for example, images are embedded in the file, and once they are there, there is no way to remember where they came from. This makes it difficult to modify the images, or see which dataset is included in said image. With SCIMAX, the data and code are included in the paper itself, so there is never any ambiguity as to where the data came from, and it is easy to modify figures right in the paper as needed, Kitchin explains.
Perhaps the main benefit of SCIMAX, though, is that is can be customized and extended to meet a researcher’s needs.
“We’ve been able to integrate bibliography/citation management, commenting/annotation, integration with dictionaries, thesauruses, speech to text, etc.,” Kitchin said. “We can connect SCIMAX to web servers, external programs and more, opening the possibility of controlling laboratory instruments from an electronic notebook. There is no other program where this is practical.”
Importantly, papers written in SCIMAX can be exported to LaTeX, which is a format accepted by many scientific journals.
Beyond simplifying report writing, Kitchin says the true goal of SCIMAX is to increase the level of integrity in scientific research by increasing replicability. The more research teams that adopt the software, the more accurate their reports will be, and the more others can build on and reuse research for problems big and small.
Photo: John Kitchin, Chemical Engineering Professor at Carnegie Mellon University. Credit: CMU