Reading discard

Non-coding RNA detection methods combined to improve usability, reproducibility and precision.
Peter Raasch, Ulf Schmitz, Nadja Patenge, Julio Vera, Bernd Kreikemeyer and Olaf WolkenhauerEmail http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-491

Has usability in the title but is tool-focused, not really usability focused.

Reading - bioinformatics tools analysis framework at EMBL-EBI

A new bioinformatics analysis tools framework at EMBL–EBI

Mickael Goujon, Hamish McWilliam, Weizhong Li, Franck Valentin, Silvano Squizzato, Juri Paern and Rodrigo Lopez* http://nar.oxfordjournals.org/content/38/suppl_2/W695.short

Why not useful?

The paper itself is fine, but focuses on describing a suite of tools with a common interface, rather than any specific usability analysis. There were a few brief notes about user friendly interactivity - wizards, meaningful error messages, etc. but this was not the focus of the paper.

The only other thing of any real note was that they had a UI and APIs, allowing both user friendly and programmatic access.

Reading: Bioinformatics meets user-centred design: a perspective

Bioinformatics Meets User-Centred Design: A Perspective Katrina Pavelin, Jennifer A. Cham, Paula de Matos, Cath Brooksbank, Graham Cameron, Christoph Steinbeck http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002554

BLU, etc. etc. I liked this bit:

“There is also a lack of incentive: it is the novelty of the tool that gets the paper published, not the UCD work associated with it. Moreover, once the paper has been published, there may be less motivation to improve the tool”

Discusses an EBI redesign focusing on users and how successful it ended up being (very).

Overall it generally makes a strong case for why usability is important, and suggests training people in ux who already have domain knowledge in software development and/or bioinformatics.

#Good for Presenting a backing case in the intro of a paper with regards to why usability needs more focus.

Reading: Beyond power: making bioinformatics tools user-centered

This is an older paper, from 2004. It’s still entirely relevant, however - it begins by pointing out just how important making usable bioinformatics tools is, alongside the fact that many people are unlikely to adopt tools with poor usability if they’re used to richer interfaces elsewhere.

The researchers in this paper redesigned the NCBI website by aiming to adhere to known design patterns (Pattern Oriented Design), alongside a set of personas.

Why is this paper useful? Mostly as a backing reference saying we need to make bioinformatics more useable.

The Enzyme Portal

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-103 Matos, Paula de, Jennifer A. Cham, Hong Cao, Rafael Alcántara, Francis Rowland, Rodrigo Lopez, and Christoph Steinbeck. 2013. “The Enzyme Portal: A Case Study in Applying User-Centred Design Methods in Bioinformatics.” BMC Bioinformatics 14 (March): 103.

This article looks to approach things from the same direction I am inclined to: looking at the background of usability and making it clear that in general within bioinformatics, usability is lacking, with several useful citations leading to locations where others have identified the same problem.

I could have quoted almost every section of the “background” in this paper, as it’s so useful. It takes into account the varying level of skills between computational biologists / bioinformaticians and wet lab scientists.

Personas: interview people who fit into personas to ensure they fit correctly, ensured they had entry and exit criteria that satisfied each persona.

They used a group workshop to discuss and identify needs in the enzyme portal, with mix of researchers, pis, phd students, etc.

paper prototype testing was followed by iterative interactive prototypes

at the end they reported specific findings about the enzyme portal, rather than generalised methods.

Overall: really good article, early stages should be cited and used as inspiration for any of my related usability related papers.

Reading - evaluating a tool's usability based on scientists' actual questions

B. Mirel, “Usability and Usefulness in Bioinformatics: Evaluating a Tool for Querying and Analyzing Protein Interactions Based on Scientists’ Actual Research Questions,” Professional Communication Conference, 2007. IPCC 2007. IEEE International, Seattle, WA, 2007, pp. 1-8.

Section 1: The intro discusses the need for bioinformatics software to help lab scientists find out more regarding the genes, proteins etc. that they are working with, and the fact that many of the available tools lack the usability to make the tools truly useful.

“Based on even this limited scope, findings show that when tools have surface level usability experimental scientists are able to readily engage in productive patterns of interaction for their research purposes. However, although they can easily find and operate features the interactions and outcomes are not ultimately useful.”

The author suggests that in order to be useful, tools need to be dedicated towards specific complex tasks. (Whilst it’s not explicitly stated, I’m inferring that overgeneralisation can harm usability and usefulness).

Section 2: Usability testing performed on bioinformatics tools is often too simplistic and doesn’t go into the depth of a real use-case, instead being a simple pre-defined task.

I may possibly be missing parts of this article, I stopped reading and came back ages later. Publishing for now.

Reading: CLI usability guidelines

Seemann, Torsten. “Ten recommendations for creating usable bioinformatics command line software.” GigaScience 2.1 (2013): 1-3. APA

This paper is written by someone with experience of CLI bioinformatics tools, covering 10 guidelines for greater CLI usability. Whilst I think I’m typically concerned with UIs, this may also be relevant.

They cover providing useful feedback a well a general programming-relevant guidelines like not hardcoding, managing dependencies, etc.

Overall these are reasonable and decent guidelines but probably not something I’ll refer to in the future.

Reading list discard

Veretnik, Stella, J. Lynn Fink, and Philip E. Bourne. “Computational biology resources lack persistence and usability.” PLoS computational biology 4.7 (2008).


Why not useful?

Sure, usability is lacking. This is known. But there is too much focus on the lack of persistence, e.g. outdated databases that aren’t maintained when grants run out. I care more about usability flaws - specifics - than the grant politics surrounding it. (Don’t get me wrong, I care about grants a lot, but I’m not sure that this is the context I’m looking for.)

Reviewed: 18 March 2016.

First reading article

Title: “Better bioinformatics through usability analysis”

Link: https://bioinformatics.oxfordjournals.org/content/25/3/406.full

More usable web applications would enable bioinformatics researchers to find, interact with, share, compare and manipulate important information resources more effectively and efficiently, thus providing the enabling conditions for gaining new insights into biological processes.

  • sets tasks to investigate gene info in CATH, NCBI, BioCarta, and SwissProt regarding a breast cancer case. Observes users & encourages to think aloud
  • find homologues in drosophila

CATH: Discusses “navigation usability”.

For large web repositories, however, the complexity of the information and navigation structures being designed and the multiplicity of micro-design interventions over time can cause designers to lose control of what is offered to the user at any given moment.

Different ages of sub-systems within a bioinformatics application can cause poor user experience - e.g. linking to old data from an up-to-date page. (Section 4.2, re CATH). User should always know what data they are working with

Section 4.4, CATH: sorting browse-only data by sub family can make it hard to find the desired item. (e.g. mystery categories, user has to manually scan them all).

Section 5, Search:

  • Alternative identifiers, e.g. spellings (oestrogen/estrogen) and synonyms of identifiers, need to be associated.
  • DBs assume knowledge of data model. “SwissProt, for example, uses names of databases to communicate the search domains: SwissProt/trEMBL, SwissProt/tremble (full), SwissProt/tremble (beta), PROSITE, NWT-Taxonomy, SWISS-2D Page, just to name a few. Instead of being able to select the ‘content domain’ to search for, the user is faced with a list of technical names of databases they may not be familiar with.”
  • Makes three recommendations for clearer searching. Inform user about:
    1. search scope
    2. ontology
    3. query syntax
  • Overlong list results mean either:

“(i) intimidated by the long list of items, they do not explore further and try to reformulate the query; (ii) they focus on the first, second or third results, hoping the first few results to be the most relevant ones (which is not always the case)”

  • “it is important to explicitly communicate to the user the actual ranking criteria used for displaying the results…. possibly, to allow sorting the obtained results by multiple, additional attributes (e.g. by publication/release date, by alphabetical order).””

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