biology

MyExperiment

MyExperiment is a biology topic covered in the lgStudy science library. This page brings together a partial reference excerpt, illustrations, worked examples, real-world applications and a short study plan, so you can understand MyExperiment rather than just read about it. In short: myExperiment is a social web site for researchers sharing research objects such as scientific workflows. The myExperiment website was launched in November 2007 and contains a significant collection of scientific workflows for a variety of workflow systems, most notably Taverna, but also other tools such as Bioclipse. myExperiment has a REST API and is based on an open source Ruby on Rails codebase.

Key takeaways

MyExperiment belongs to biology; place it in that map before memorising details.
Learn the definition first, then one example that makes the definition concrete.
Connect MyExperiment to a quantity you can measure, compute or draw — that is where exam questions come from.
Reproduce the core statement of MyExperiment from memory before moving on to harder problems.

Reference excerpt

myExperiment is a social web site for researchers sharing research objects such as scientific workflows. The myExperiment website was launched in November 2007 and contains a significant collection of scientific workflows for a variety of workflow systems, most notably Taverna, but also other tools such as Bioclipse. myExperiment has a REST API and is based on an open source Ruby on Rails codebase. It supports Linked data and had a SPARQL Endpoint, with an interactive tutorial.

Origin The myExperiment project was initially directed by David De Roure at University of Southampton (later University of Oxford) and was one of the activities of the myGrid consortium led by Carole Goble of The University of Manchester, UK and of the e-Research South[link removed] UK regional consortium led by the Oxford e-Research Centre. It was originally funded by Jisc under the Virtual Research Environment programme and by the Microsoft Technical Computing Initiative.

Capturing digital experiments While the initial idea of myExperiment may have been to capture computational experiments as executions of registered workflows (submitted to a configured workflow runner API), in reality most users of myExperiment shared only workflow definitions, possibly with example files.

Influence on Research Objects development The myExperiment Ontology included details of social networking, attributions, experiments and workflow structures. This work was instrumental in forming the idea of Research Objects, a Linked Data method for identification, aggregation and exchange of scholarly information. In the myExperiment Ontology, the Research Object was loosely represented as a "Pack" of typed related resources, including workflows. myExperiment was since enhanced by the Workflows Forever project (Wf4Ever) which in 2011 aimed to provide new features to support the preservation of Research Objects in conjunction with the dLibra digital library framework. The Wf4Ever co-development with the workflow system Taverna (at the time maintained by myGrid), led to the creation of the Research Object Model ontologies. RO Model uses many of the conceptual ideas of the myExperiment Ontology, but with a basis of an OAI-ORE aggregation as the central digital object, and with a primary goal of reproducibility and integration with the W3C provenance model PROV, the replacing RO Model was independent of the social network at a workflow registry. In 2019, subsequent development of Research Object Crate (RO-Crate) replaced the RO Model with a profile of schema.org serialised in JSON-LD, this was general purpose for scholarly outputs. This ontology-less approach was better suitable for packaging in a ZIP archive and aimed to be more approachable for developers without Linked Data experience.

Current status The myexperiment.org is as of 2024 hosted by University of Manchester, at professor Carole Goble's eScience Lab as a legacy service. The research group has since launched myExperiment's replacement, the workflow registry workflowhub.eu, which uses a profile of RO-Crate for publishing workflows together with their context and dependencies. In contrast with myExperiment, the WorkflowHub however do not focus on the social network aspects (beyond institutional/project organisation of entries), and do not attempt to capture any experiments.

References

Worked examples

Example 1 — a first encounter with MyExperiment

Start with the simplest possible case. Write down what MyExperiment claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In biology, the smallest case is usually a single object, a single equation or a single measurement. Check that every symbol or term in your sentence has a meaning in that case.

Example 2 — changing one variable

Take the situation from Example 1 and change exactly one quantity: double it, halve it, or set it to zero. Predict what should happen to MyExperiment before you calculate. Comparing your prediction with the result is the fastest way to find out whether you understand the idea or only the words.

Example 3 — an exam-style question

Typical questions about MyExperiment ask you to (a) state it precisely, (b) apply it to given data, and (c) explain a limitation. Practise writing all three answers in under five minutes; the third part is what separates a full-mark answer from an average one.

Applications of MyExperiment

In research: MyExperiment appears in biology research whenever the underlying quantities have to be modelled precisely. Papers usually cite it as a starting assumption and then explore where it breaks down.
In technology and industry: Engineering practice reuses MyExperiment in design rules, simulations and safety margins. Knowing the idea lets you read a specification sheet and understand why the numbers look the way they do.
In the classroom: MyExperiment is common in secondary-school and first-year university syllabi. It links to neighbouring topics Biological databases, Department of Computer Science, University of Manchester, Jisc, so understanding it makes those chapters shorter.
In everyday life: Look for MyExperiment outside the textbook — in sport, cooking, traffic, electronics or the sky above you. An example you found yourself is remembered far longer than one you were given.

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How to study MyExperiment in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what MyExperiment means in your own words.
Compare your version with the excerpt and mark what you missed.
Work through the three examples above with pen and paper.
Explain MyExperiment out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is MyExperiment in simple terms?

Why does MyExperiment matter?

Because it connects several biology ideas at once: it gives you a definition you can apply, a quantity you can calculate, and a way to check whether a result is plausible.

How should I study MyExperiment?

Read the excerpt, restate it from memory, then work through the examples and applications listed on this page. The five-step study plan above takes about twenty minutes.

What does this page cover?

It gives you a compact reference excerpt plus original lgStudy explanations, examples, applications and study material on MyExperiment.