Good Usability Practices in Scientific Software Development
Scientific software often presents very particular requirements regarding usability, which is often completely overlooked in this setting. As computational science has emerged as its own discipline, distinct from theoretical and experimental science, it has put new requirements on future scientific software developments. In this paper, we discuss the background of these problems and introduce nine aspects of good usability. We also highlight best practices for each aspect with an emphasis on applications in computational science.
Best Practices, Usability, Scientific Software, Computational Science, Software for Science.
Scientific software development is a field of growing importance but lacks a widespread methodology. Scientists generally have little or no training in software engineering but tend to be main developers of computational science codes. They face a number of challenges including: quickly changing requirements due to the research nature of the work, competition between maintainable and performance code, and lack of metrics that would reward investment into sustainable software [1, 2]. Of particular detriment is the pressure to rapidly produce scientific publications [3, 4]. It may be possible to overcome this publication pressure when funding agencies are convinced that it is worth investing directly in software software for computationally intensive fields. The Science and Technology Facilities Council (STFC) in the UK Collaborative Computational Projects (http://www.ccp.ac.uk/about.html) sets a good example.
In this work we focus on usability, a particular aspect of software development and design. Usability is one of the attributes of sustainable software and can be defined as “the extent to which a product can be used by specified users to achieve specified goals with effectiveness, efficiency, and satisfaction in a specified context of us” [5, p.3]. Without proper usability, a software cannot be distributed and applied even within its targeted domain. More importantly, its unusable software can easily result in non-reproducible science and the violation of the FAIR principles . Unfortunately, usability is often neglected in scientific software development , and is of mixed perceived importance to users and developers [8, 9]. Scientific software usage and development present many challenges for usability design that can be related to development models, user-base needs and specialization, professional practices, technical constraints, and scientific demands . Computational science is therefore an idiosyncratic field with unique and, occasionally, counterintuitive usability requirements. There are, nevertheless, a significant number of informative case studies and guidelines on the subject [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 7, 22, 23, 24]. Supported by those references and informed by first-hand experience, we discuss usability challenges and how to address them.
2 Good Practices
2.1 Think Beyond Graphical User Interfaces
Graphical user interfaces (GUIs) have made software user-friendly and
arguably fosteed the popularization of software in general. However, scientific
software might require alternatives that, if not more intuitive, are more
appropriate and efficient depending on the user’s needs — especially if they
involve entering a large amounts of data, and reading the data from many files,
or running on a shared or distributed architectures.
Command-Line Interfaces (CLIs) are popular in computational science because they
often allow for quick repetition of tasks  and scriptability.
The analysis of large datasets can be significantly easier and more productive
when done through command-line input than through visual-based interfaces .
Even for software where daily use relies on a GUI, such as text processors and web browsers, there are times when having a CLI for some tasks is a time saver. For example, users of LaTeX, or the LibreOffice or Chrome CLIs can convert a text document into PDF format from the command line.
2.2 Keep UI Code Separate From Scientific Calculation
Simulation (or any scientific calculation) should not be embedded in User Interface (UI) code . This rule is particularly true for scientific software primarily because, as previously stated, scientific software should be usable via a number of alternative interfaces, such as GUI and CLI. Moreover, it should be possible to access these interfaces both locally and over a network (e.g., via ssh). Keeping the scientific calculation code wrapped into functions that are called by the UI should make reconfiguration and customization more convenient , make porting the functionalities to another UI easier and make integration with other software simpler.
2.3 Keep the Configuration in a File
Some tasks requires researchers to provide a long list of parameters to define their computational problem, and the software they are using may not provide default values for the parameters, or the default parameters need to be overriden. In these situations, it is very handy to have the ability to store some or all of the parameters in a configuration file that the software can read at the begining of every execution. Alternatively, if a command line tool asks for input parameters from the standard input, which requires continuous user interaction, it can be modified to be scriptable. In a script, the configuration parameters are stored next to the execution command itself .
Configuration files have the advantage of being declarative and automatically verifiable. The file defines a state which the program will start from or try to achieve, rather than a procedure which leads to that state. Moreover, a parser can automatically check to see if state is valid. The former is good for reproducibility because it is (ideally) unambiguous even years later . The latter is good for accuracy because the code can check if the parameters in the file are sensible . This state-based approach can also make parallelism easier to automatically reason about  and some parallel runtime environments have made use of this property [35, 36].
Domain Specific Languages (DSLs), on the other hand, provide additional flexibility not present in a plain configuration file. They allow the user to programmatically define new behaviour for the code. This can be a major advantage since it often enables the code to be extended to unforeseen use-cases without major rewrites. DSLs can also allow the user to interact with the code at runtime, which can be helpful for debugging, prototyping, and visualization . The syntax and rules of the DSL can also provide the same error checking as a parameter file.
While defining a new domain specific language (DSL) requires the development of a parser for the language, this extra effort can be avoided by embedding the domain specific language in an existing general purposes language. This has been demonstrated by a number of projects recently, and Python is a common choice as the general purpose language. In this context, the domain specific language is given through a Python module that the user imports into their generic Python program, and which provides commands, objects and operations that are specific to the domain in question. The Python program then becomes the (very flexible) configuration file for the computational problem.
However, some care is required when designing such DSLs: the elements of the DSL must be constructed so that users cannot combine them in ways that would take the tool outside its range of applicability. This could be achieved through explicit assert statements in the DSL’s implementation or appropriate (often Object Oriented) design. If the code author lacks the experience or time available to achieve this, it is important to document the assumptions made for use of the DSL so that it is not used incorrectly inadvertently by others in the future. For example, the yt project  is a DSL for scientific visualization and data analysis built in Python. If the data fed into yt doesn’t satisfy the correct assumptions, yt could produce spurious visualization artifacts or incorrectly integrate a quantity over the domain. Therefore the authors of yt take extreme care to document their API, sanitize their inputs and throw informative error messages when incorrect data is fed into the tool. A major part of this process is unit testing the DSL’s functionality
2.4 Design for Small, Incremental Changes
Making incremental changes is considered a best practice for scientific software development , and the same principle applies to user interfaces. Ideally, UIs should be planned for extensibility and frequent changes as new requisites emerge. Through incremental changes, software is more likely to stay attuned to users’ needs, not forcing them to radically change the way they work .
Regarding constant updates and addition of new functionalities, UI components that can be easily extended might offer interesting solutions. This is the case for map3D, a scientific visualization software for displaying and editing three-dimensional models and associated data . During development, pop-up menus were implemented for providing the necessary flexibility, allowing developers to add new commands and submenus as the software development and requisites evolved . It is worth mentioning that web-based applications might take advantage of the modularity allowed by frontend design methodologies such as Atomic Design , making it easier to configure user interfaces as the project advances.
The parameter files and DSLs described in section 2.3 are particularly good for satisfying this design constraint. For example, the Einstein Toolkit  packages low-level code in modules. Each module must declare which functionality it adds, which relevant parameters can be set in the parameter file, and how these parameters depend on other modules. The parameter file parser then automatically adds these options to the parameter file at compile time. The yt project  provides a DSL for scientific visualization. This DSL interacts with the low-level code only through function calls and so functionality can easily be incrementally added by the introduction of new DSL language features or functions.
2.5 Facilitate and Register User Activity and Environment
There are a number of ways through which usability can be enhanced based on past user activity. First, providing access to a list of recent commands and allowing users to re-execute them can help users save time. This is a major reason for the popularity of command-line interfaces . A very popular implementation of this concept is the ability to access previously typed commands by pressing the up arrow key or do a reverse search on the history of executed commands. Users can also press the right and left arrow keys to navigate through a previous command and edit it to suit their needs. Second, it might be a good idea to give users quick access to frequently used commands . In some environments, the tab key is used to roll among frequent used commands or to auto complete a command. Third, logging user activity might help users identify and support research reproducibility  by exporting the history to a file.
After registering user activity, developers can go further and log the user environment, i.e. compiled binary, configuration files, input files and output files, used when running the program. This is useful in scientific software since the output of any experiment can be different because of different implementations (or compiler optimizations) of the Basic Linear Algebra Subprograms (BLAS), LAPACK (Linear Algebra Package) or any other library used when performing the experiment. This automatic logging not only provides users quick access to their exact configuration for debugging purposes but also allows the computation to be reproduced years after it was run for the first time. One example framework is Formaline . For software developers working with Python, we mention the related packages ReciPy  and Sumatra .
2.6 Learn About How Users Work
Guidelines and case studies often recommend the adoption of a user-centered design process that seeks to develop a firm understanding of how scientists do their work before developing a piece of software. This understanding can be acquired by learning the meanderings of scientific work , or through a participatory design approach in which users are actively involved in the design process [16, 46, 47, 48]. It is also important to analyze the scientific work within the environment where it actually takes place  and evaluate existing tools which are already in use . In this last case it might be advantageous to adopt preexisting industry standards (e.g.: keyboard shortcuts for common functionalities, iconography, etc.).
When designing user interfaces for scientific software, it is a good idea to address specific users or user-bases rather than aim for a general solution [14, 19]. Ideally, GUIs should be open to user customization and adjustable to personal preferences and professional specialization [49, 14]. However, users should not be overwhelmed by an excessive number of customizable parameters — some of which can be unimportant or meaningless to their specific case. Instead, there should be an additional section for setting advanced parameters .
As a user base grows, users may have suggestions for improving the UI or the underlying scientific code. If the code is open source, it can be extremely advantageous to transform these users into developers so that they can bring their user experience and domain expertise to bear . Additionally, it is advisable that scientific domain experts are brought into the design process for informing domain best practices [15, 21] and evaluating the tool .
2.7 Be Minimalistic, but Look Out for Exceptional Needs
Designers should be attentive to information that is particularly relevant in scientific software, but that could be eluded otherwise. Metadata, for instance, is often required to be readable and easy to access [17, 51, 18, 20, 25, 47].
Also, despite recent trends favoring flat design over skeuomorphism (i.e.: visual design that imitates the appearance of real-world objects), software versions of physical instruments might benefit from adopting the looks of their real-world counterparts , making it easier for users to recognize and learn about their functioning. An example for that approach is LabViEW’s set of GUI components mimicking dials, knobs and meters .
Finally, minimalism should emphasize, rather than conceal, critical information such as system malfunctioning , emergency information , and situations where awareness and response under time pressure are essential. For instance, the Sky software for astronomical visualization reduces users’ cognitive load by simplifying three-dimensional visualization data as a two-dimensional projection .
2.8 Design for Precision
In order to achieve satisfying results, scientific work often demands precision regarding user’s input. A possible means for that would be continuously constraining users’ input and providing feedback on it. The Dynamic Dragging Interface, for instance, makes user of force-feedback input devices to help users selecting sections of 3D brain visualization . Another solution would be not accepting the input when the input device, such as a stylus or mouse, moves too fast.
It can be advantageous to have two input modes for the same action — one designed for accuracy, and another for speed. In map3D, for instance, geometric models could be moved, rotated and scaled through dial boxes (accurate, but slower) or, alternatively, via mouse (less accurate, but faster) . Another approach would be to give users a way to switch between fast and precise working modes. For instance, by activating a ’snap’ mode where the mouse cursor snaps to a gridline, objects or other elements on screen.
2.9 Contextualize User Actions
Work in scientific software can involve a number of different and/or sequential tasks to be performed by users. In those cases, it is desirable to contextualize users’ actions, facilitating their access to functions that are relevant to their current tasks and preventing their access to functions that are not.
The Petri Net Toolbox for MATLAB, for instance, features a button that toggles between Draw Mode, for creating and editing models, and Explore Mode, for simulation and analysis . When switching between modes, GUI elements are displayed or hidden depending on their relevance to the selected mode. This approach is known as a design pattern named Disabled Irrelevant Things .
Another possible approach is the Window Per Task  design pattern, in which tasks are distributed across individual screens containing the appropriate commands for that task only. Pharmaceutical biology software Lipid-Pro makes use of this design pattern by organizing its tasks into separate panels .
Throughout the previous section, we have presented a nonexhaustive set of good practices in usability for scientific software, taking in consideration challenging aspects of scientific software development and use such as the lack of attention to software engineering; the need for reproducibility; the handling of large amounts of data; the complexity of actions and parameters involved in scientific work; frequent changes in requirements; particularities of scientific work and its environment; the need for accessing and responding to critical information; and the importance of precision.
By adopting the presented practices, developers should be able to deliver applications that are more usable, robust and more appropriate for scientific work.
This project began during the Fourth Annual Workshop on Sustainable Software for Science: Practices and Experiences (WSSSPE4), where four of the authors established the Working Group on Software best practices for undergraduates . The authors would therefore like to thank the organizers of WSSSPE4 for facilitating this conversation. J. Miller and F. Queiroz would like to thank travel grants from the National Science Foundation of the USA and The Gordon and Betty Moore Foundation, which made attendance possible. J. Miller also acknowledges support from the Natural Sciences and Engineering Research Council of Canada and from the National Science Foundation of the USA (OCI 0905046, PHY 1212401). Research at Perimeter Institute is supported by the Government of Canada through the Department of Innovation, Science and Economic Development and by the Province of Ontario through the Ministry of Research and Innovation. F. Queiroz acknowledges support from PUC-Rio and Tecgraf Institute. H. Fangohr and R. Silva acknowledge support from the Software Sustainability Institute and Engineering and Physical Sciences Research Council (EPSRC) in the UK.
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