Prism 10 introduced an all new file format that unlocks an enormous amount of potential as to what can be done with Prism files - both inside and outside of the application - while making sure that the transition from using one of Prism's older file formats is nearly seamless. This page covers the philosophy and motivation behind the decision to introduce our new file format, and also provides some technical details on how the new file format is organized and how - if you choose - you can explore it!
Philosophy and motivation behind the new file format
More Open, More Accessible
Prism files contain an enormous amount of useful information about your work: from your raw data, to the analyses options that you've selected and the subsequent results, to the customized graphs that you create. But ultimately, this is all your work. And we believe that you should always have complete access to it. This was one of the primary motivations for us to introduce the new .prism file format as a means to make it easier to access these assets within the file itself.
Fundamentally, what has changed with the new Prism file format? First and foremost, the contents of your file are no longer hidden or obscured behind a proprietary format. Instead, all of the content inside the new Prism file format is stored within structures that can be fully explored and exampled (the new Prism file operates much like a zip file). Moreover, we chose to use industry-standard methods for storing each component of the file: data are stored in CSV format and all analysis parameters and results are stored in standard JSON schemas. Ultimately this means that nothing gets locked away inside a file that can only be accessed if you're using Prism.
Transparency is key
Validation of scientific results is a critical component of any research project. This often means re-creating or repeating the work that was performed, using the same experimental conditions, the same data collection methods, and the same analysis procedures to reproduce the same results. Unfortunately, the inability to reproduce results - especially in biological, biochemical, and biomedical research - has become a common problem known as the "Reproducibility crisis". Importantly, this problem often has nothing to do with whether or not the results are "correct". Instead, the problem is due to the lack of transparency surrounding the methods used for data collection and analysis. When this information is unavailable or incomplete, even minor changes to the experimental process can lead to dramatically different (and thus, non-reproducible) results. This is another reason that we've chosen to transition Prism to a more open file format: every selected option for every analysis is readily available alongside every parameter and calculated analysis result. Your Prism file will provide a clear lineage of your analysis work all the way from input data to final results and visualizations.
Embracing FAIR ideologies
In 2016, an article titled "The FAIR Guiding Principles for scientific data management and stewardship" was published in Nature's Scientific Data journal and introduced the concept of FAIR data principles. The objective of these principles was to increase the Findability, Accessibility, Interoperability, and Reusability of scientific data which would - in turn - help improve the reproducibility of any work performed with the data. As part of the transition to our new file format, we have embraced much of the FAIR ideology. Any component of a Prism file (data, analysis parameter, or result) can be located within our file structure, and is available for re-use in any desired subsequent manner.
Whether you've just started using Prism or have been using it for decades, we know how important it is to retain access to your results (after all, this is why we chose to move to a new file format in the first place!). So we definitely didn't want you to lose access to any Prism files that you generated in one of our older file formats (with the .pzfx or .pzf file extension). But we also wanted to make sure that introducing a new file format would be as seamless as possible.
That's why we introduced "Compatibility Mode" with Prism 10. Essentially Prism 10 will allow you to open files in older formats in Compatibility Mode without warnings or alerts. Opening in Compatibility Mode won't limit you: you'll still have access to everything Prism 10 has to offer. Importantly, when you choose to save the file, Prism will automatically check to ensure that the file is still compatible with its existing file format. If there are no compatibility issues, Prism will simply save the file as you would expect. If any new functionality or features that are incompatible with the old file format are present, Prism will list each of these issues and provide you with options on how to proceed (including saving the file in the new .prism file format). These changes ensure that you can seamlessly transition to using our new file format without any worry about what happens to all of your existing work.
