Abstract
Visualization - the process of interpreting data into visual forms - is increasingly important in science as data grows rapidly in volume and complexity. A common challenge faced by many biologists is how to benefit from this data deluge without being overwhelmed by it. Here, our main interest is in the visualization of genomes, sequence alignments, phylogenies and systems biology data. Bringing together new technologies, including design theory, and applying them into the above three areas in biology will improve the usability and user interaction. The main goal of this paper is to apply design principles to make bioinformatics resources, evaluate them using different usability methods, and provide recommended steps to design usable tools.
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Acknowledgements
Special thanks to all the participants assisting voluntarily with the survey, observation and interviews. We thank Anna Croon Fors and Hannele Tuominen for extensive support and feedback. We are also very grateful to PlantGenIE and UPSC Bioinformatics teams for helping with the design and development of tools and Niklas Mähler for the design of Figure 3.0.
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Appendices
Appendix A - Survey Questions
A. Learnability
-
1.
This tool is easy to use.
-
2.
It works according to my initial requirements.
-
3.
This tool is user friendly.
-
4.
I can use the tool without written instructions.
-
5.
It provides a flexible tour guide.
-
6.
The display layouts are consistent between tools.
-
7.
The label format is consistent.
-
8.
The ordering of menu options is logical.
-
9.
The grouping of other PlantGenIE tools are reasonable for easy learning.
-
10.
Help covered user requirements.
B. Memorability
-
1.
Required input is entered only once.
-
2.
Letter codes for menu selection are designed carefully.
-
3.
It remembers the correct number of genes.
-
4.
Icons and symbols are helpful.
-
5.
I can easily remember how to use it.
-
6.
It provides easily distinguished colors.
C. Efficiency
-
1.
This tool helps me to conduct my analysis more effectively.
-
2.
This tool helps me to share analyses with others.
-
3.
This tool helps me to easily reproduce my results again and again.
-
4.
It provides comprehensive search.
-
5.
It provides a Close or Cancel button when required.
-
6.
Results of my analysis are compatible with my expectations.
D. Satisfaction
-
1.
This tool meets my needs.
-
2.
Both occasional and regular users would like it.
-
3.
It works the way I want do in my analysis.
-
4.
I am satisfied with the tool functions.
-
5.
Result display is consistently according to my expectation.
-
6.
I would recommend it to a friend.
E. Error and Feedback
-
1.
It is easy to find the contact us form.
-
2.
It provides explicit entry of corrections.
-
3.
Error messages are helpful.
-
4.
Completion of processing is indicated.
-
5.
I can recover from mistakes quickly and easily.
-
6.
It provides UNDO to reverse control actions.
Suggestions (Free text fields)
-
1.
What can we do to improve the functionality of the tool?
-
2.
What can we do to improve the appearance of this tool?
-
3.
Do you have any other suggestions?
-
4.
What, if anything, do you find frustrating or unappealing about this tool?
-
5.
What is your main reason for using this tool today?
Appendix B - Questions and Answers to Free Text Survey Questions
-
(1) What can we do to improve the functionality of the tool?
exNet doesn’t work sometimes.
Improvement in Blast link to gbrowse is expected since sometimes it does not work.
Better to have more help tutorial videos.
Unsure
Identify if any suggestions are arised in surveys by different users.
Better to have more user guidelines
Could you please provide more detailed information?
Write some good help tutorial
It’s great if snp information can be added into gene pages.
It’s great if you can improve this tool by enabling to add more species
Functionality is excellent. Just I will add some quick instruction for firs step for use the app.
Is it possible to add version 1.1 access to populus trichocarpa genome?
Replacement with Adobe flash tools with JavaScript is great adding to the site
Sometimes Exnet export and sample lists are not functioning. Please note for improvement.
More user instructions are needed
Need to improve the list of example gene list for different aspen assemblies which is missing.
Would be great if you could make it possible to match PU numbers also to Potri v3 gene models without the intermediate step going through v2 models.
If this can be improved to integrate Galaxy into Plantgenie that would be nice.
I would like you to integrate CDNA and protein expression data (blast) for all likes like for Potri.
-
(2) What can we do to improve the appearance of this tool?
It’s OK
Fonts. Another one and more bigger (like this form). Improve general design. Looks very technical (not designed).
NA
Looks great!
-
(3) Do you have any other suggestions?
Sometimes searching for different aspen genome is not working. Please fix this.
Nope
try with different web browsers
It’s nice if there is a latest news and updates page
Please have a introductory course online.
-
(4) What, if anything, do you find frustrating or unappealing about this tool?
write an email
gene lists sometimes does not work.
My big frustration is that I don’t know nothing about genes and plants.
Im satisfied
Nothing so far!
I’m happy with using this tool.
-
(5) What is your main reason for using this tool today?
User friendly and helpful for efficient research results.
Very supportive for my work
Look at a gene annotation
This tool makes my research analysis work easy and it saves time.
easy and time saving analysis of data
Effective and efficient
Accuracy of analysis of results
Easy analytical support
check genes in my lists
Excellent
Test
Especially conversion between different gene accession numbers. This is the best tool there is for it! Great work!
genelist
phylogenetic studies not today but generally. and sometimes expression information.
Work!
Appendix C - Usability Questions used in the Office
-
1.
Have you use this tool before?
-
2.
What is the first impression regarding the tool?
-
3.
Could you identify what the tool is all about?
-
4.
Could you find this as an useful tool?
-
5.
How intuitive & helpful is the navigation?
-
6.
Do you find any Issues with functionality and design?
-
7.
Was anything too well hidden in the tool interface?
-
8.
Do you find problem with the color scheme?
-
9.
Is it easy to read (font style & size)?
-
10.
What are the things you like most in this tool?
-
11.
What can be improved?
Appendix D - Answers to Questions asked in the Office
8 people have answered to the usability questions.
Have you use this tool before?
8 out of 8 people have use the people have used the PlantGenIE
What is the first impression regarding the tool?
To do the analysis
Beautiful
Confusing
Need more help pages
Easy to use compare to other tools
No connection between different sites
Could you identify what the tool is all about?
6 out of 8 have identified the functionalities of different tools (exImage, exNet, exPlot and GeneList). Others could not find some of the functionalities.
Could you find this as an useful tool?
6 out of 8 said yes other 2 are not sure about the functionalities or usability.
How intuitive & helpful is the navigation?
Helpful
to some extent
good to have more help guidance
Do you find any Issues with functionality and design?
Some tools are not adopted to different screen sizes
Was anything too well hidden in the tool interface?
Icons are not clear
good to have tooltips
Do you find problem with the colour scheme?
Why green only
Its good for eye
I have no problem
Is it easy to read (font style & size)?
Fonts. Another one and more bigger.
Improve general design.
Looks very technical.
Looks great!
What are the things you like most in this tool?
Very supportive for my work
Look at a gene annotation
Accuracy of analysis of results
This is the best tool there is for it! Great work!
What can be improved?
gene lists sometimes does not work.
Im satisfied
Nothing so far!
I’m happy with using this tool.
conversion between different gene accession numbers.
Appendix E – Initial Expert Review Without a Checklist
January 10, 2016
Website review for http://popgenie.org
“This has to be one of the most interesting sites I have been to in a long time. Honestly, this type of information is beyond my knowledge of this particular subject. Today, January 11, 2016, I introduced this website to a co-worker, who is the Jr. High Science teacher at the school where I work. I asked him to go through it as he had time and tell me his thoughts about the site later in the week.
Upon landing on the home page, I was intrigued with all the colors and how the blank space allowed the information to be broken into clusters that anyone can follow through. The most important thing I noticed, throughout the entire site, the option to “take a tour” of the present page is available- of which I used very frequently. The reason I used this option was to learn more about the way the website was intended for use by the user. There are many options for one to increase their knowledge in this topic with the use of this site.
The PDF poster is magnificent! I studied it for quite some time. This is a piece of information worth printing and using as a reference. It may not be intended for that purpose for a person who is very familiar with this topic, but a someone new- I always print and take notes in order to gain knowledge of the topic and this is a poster I would want to have on hand.
I had fun playing with the different genes and plugging in information. Thank you for the sample workflow page. It provided me an example to go by when plugging in various bits of information. I went from page to page, clicking on a variety of links just to see what I might do next.
I believe this site is ideal for those who are interested in learning about plant genes and the breaking down of the information. This would be something our science teacher may want to incorporate within in class when it comes to the plant life chapter. It will provide an extra hand on opportunity to do research with his students.
During my time on the popgenie site, I found no glitches. The site is user friendly in regards to the tours and easy to read information presented in small clusters. I do not know who did your site, but it moves effortlessly, even with much information to be displayed, it loads quickly.
Thank you so much for allowing me to take part in this. Please keep in touch to update me on your study and research.”
Screencasts can be found at YouTube®[https://youtu.be/pXLtBFAYf6k].
Two interface professionals evaluated the PopGenIE tool and recorded screencasts. Screencasts can be found at YouTube®[https://youtu.be/pXLtBFAYf6k].
Appendix F - Initial Version of ComPlEX Tool and Active User Statistics Before and After Redesigning the Tool
Appendix G - A Low Fidelity Prototype has been used to Understand the Visual Representations and Locations of Essential Tool Components in ComPlEX
Appendix H - Affordances, Signifiers, Feedback, Mapping, and Constraints are Some of the Basic Design Principles Components
Appendix I - Heatmap of Survey Questions and Answers. X-axis Shows the Questions and Y-axis Shows the Participants. Color Represent the Strong Agree to Strong Disagree Options.
Appendix J - PopGenIE User Behavioral Flow for Last Year (2017/02/31–2018/02/31).
Appendix K - Survey Users by User Profession
Audience type | Number of participants |
|---|---|
Plant Biologist/Botanist | 22 |
Biologist - General | 16 |
Bioinformatician | 12 |
Computational Biologist | 5 |
Plant Data Curator | 1 |
Other | 1 |
Total (participants) | 57 |
Appendix L - Survey Users by Occupational Type
Users by profession | Number of participants |
|---|---|
Graduate researcher | 21 |
Postdoctoral researcher | 19 |
Research scientist | 8 |
Bioinformatics analyst | 5 |
Undergraduate researcher | 3 |
SW Developer/Engineer | 1 |
Total (participants) | 57 |
Appendix M - Average PlantGenIE usage by survey participants
Average usage | Number of participants |
|---|---|
Daily basis | 31 |
Weekly | 21 |
Monthly | 2 |
A few times a year | 1 |
Rarely or never | 2 |
Total (participants) | 57 |
Appendix N - Tasks for the Tests at the Bioinformatics Office
Number | Tasks |
|---|---|
1 | How many “cellulose synthesis” genes can be found in Poplulus trichocarpa? |
2 | What is the Populus tremula best Blast hit for “Potri.001G266400” gene |
3 | Can you share current gene search results with someone else? |
4 | Can you BLAST “Potri.001G266400” protein sequence and find the Best Blast hit in Poplus tremula? |
5 | Are roots highly expressed in Potri.013G082200 gene in exImage Populus trichocarpa tissue? |
6 | How to save “cellulose synthesis” genes into PopGenIE GeneList? |
7 | How to download protein sequence for Potri.013G082200 gene? |
8 | How to generate heatmap for current genelist? |
Appendix O - Usability Heuristics Selected for PopGenIE GeneList Tool Review Based on Jakob Nielsen’s Usability Principles
Number | Usability heuristics |
|---|---|
1 | Visibility of system status |
2 | Match between system and the real world |
3 | User control and freedom |
4 | Consistency and standards |
5 | Error prevention |
6 | Recognition rather than recall |
7 | Flexibility and efficiency of use |
8 | Aesthetic and minimalist design |
9 | Help users recognize, diagnose, and recover from errors |
10 | Help and documentation |
Appendix P - Summary Results of Five Usability Components
Learnability | Percentage |
|---|---|
Strongly agree | 77.9% |
Agree | 13.1% |
Neither agree nor disagree | 5.7% |
Disagree | 1.4% |
Strongly disagree | 1.9% |
Memorability | Percentage |
|---|---|
Strongly agree | 82.6% |
Agree | 9.2% |
Neither agree nor disagree | 4.4% |
Disagree | 2.9% |
Strongly disagree | 0.9% |
Efficiency | Percentage |
|---|---|
Strongly agree | 81.8% |
Agree | 10.2% |
Neither agree nor disagree | 4.4% |
Disagree | 3.0% |
Strongly disagree | 0.6% |
Satisfaction | Percentage |
|---|---|
Strongly agree | 80.9% |
Agree | 13.6% |
Neither agree nor disagree | 2.8% |
Disagree | 2.4% |
Strongly disagree | 0.3% |
Errors and Feedback | Percentage |
|---|---|
Strongly agree | 84.5% |
Agree | 8.8% |
Neither agree nor disagree | 4.4% |
Disagree | 1.9% |
Strongly disagree | 0.4% |
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Mannapperuma, C., Street, N., Waterworth, J. (2019). Designing Usable Bioinformatics Tools for Specialized Users. In: Rocha, Á., Ferrás, C., Paredes, M. (eds) Information Technology and Systems. ICITS 2019. Advances in Intelligent Systems and Computing, vol 918. Springer, Cham. https://doi.org/10.1007/978-3-030-11890-7_62
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