40 Matching Annotations
  1. Last 7 days
  2. May 2022
    1. The paper describes four ontologies for representing workflows in Research Objects, and includes examples and motivation scenarios.

      The ontologies developed make use of and extend existing well known ontologies, namely the Object Reuse and Exchange (ORE) vocabulary, the Annotation Ontology (AO) and the W3C PROV ontology (PROVO). We illustrate how the ontologies can be utilized using a real-world scenario, in which scientists created a Workflow Research Object for an investigation on the Huntington's disease. We also present the tools we developed for managing Workflow Research Objects.

      A sketch depicting the main steps that the bioinformatician followed for manipulating and analyzing datasets, and the workflows that were used in each step

  3. Apr 2022
    1. Since most of our feeds rely on either machine algorithms or human curation, there is very little control over what we actually want to see.

      While algorithmic feeds and "artificial intelligences" might control large swaths of what we see in our passive acquisition modes, we can and certainly should spend more of our time in active search modes which don't employ these tools or methods.

      How might we better blend our passive and active modes of search and discovery while still having and maintaining the value of serendipity in our workflows?

      Consider the loss of library stacks in our research workflows? We've lost some of the serendipity of seeing the book titles on the shelf that are adjacent to the one we're looking for. What about the books just above and below it? How do we replicate that sort of serendipity into our digital world?

      How do we help prevent the shiny object syndrome? How can stay on task rather than move onto the next pretty thing or topic presented to us by an algorithmic feed so that we can accomplish the task we set out to do? Certainly bookmarking a thing or a topic for later follow up can be useful so we don't go too far afield, but what other methods might we use? How can we optimize our random walks through life and a sea of information to tie disparate parts of everything together? Do we need to only rely on doing it as a broader species? Can smaller subgroups accomplish this if carefully planned or is exploring the problem space only possible at mass scale? And even then we may be under shooting the goal by an order of magnitude (or ten)?

  4. Feb 2022
    1. In hindsight, we know why they failed: The ship owners tried tointegrate the container into their usual way of working withoutchanging the infrastructure and their routines. They tried to benefitfrom the obvious simplicity of loading containers onto ships withoutletting go of what they were used to.

      Ahrens makes a useful analogy: the reason that early attempts at shipping containers failed was because their users tried to fit them into their own way of doing business instead of reorganizing their businesses to accommodate the shipping container. Similarly one needs to consider how one's note taking method fits into their work in a more integrative way. Without properly integrating it into one's workflow seamlessly the system will fail.

    2. And if you stumble upon one idea and think that it might connect toanother idea, what do you do when you employ all these differenttechniques? Go through all your books to find the right underlinedsentence? Reread all your journals and excerpts? And what do youdo then? Write an excerpt about it? Where do you save it and howdoes this help to make new connections? Every little step suddenly

      turns into its own project without bringing the whole much further forward. Adding another promising technique to it, then, would make things only worse.

      Keeping one's notes across multiple modalities, in different locations, different apps is a massive problem portending imminent and assured failure. Regardless of the system employed (paper, digital, app), one of the most important features of any note taking system is having them all centralized in one location.

    3. Writing is not what follows research, learning or studying, it is themedium of all this work. And maybe that is the reason why we rarelythink about this writing, the everyday writing, the note-taking anddraft-making.

      Here in a nutshell is the thrust of the entire book to come!

      Notes allow one to do small pieces of work over time, then by editing one's notes together to weave a story or create a broader thesis, one is primarily ordering and editing their prior work which isn't as difficult as staring at a blank piece of paper and wondering where to begin.

  5. Jan 2022
    1. What does a Functional Design have to offer? https://en.itpedia.nl/2019/01/16/wat-heeft-een-functioneel-ontwerp-te-bieden/ A functional design is a specification of the functions of the software that the end_users have agreed to. Many companies have a software_developer handbook that describes what topics a functional design should cover. This article looks at the steps of functional design in the context of software development.

  6. Nov 2021
    1. https://diggingthedigital.com/abonneren-op-aantekeningen/

      I like the idea here of being able to watch over someone's shoulder quietly to see what they're working on and how they're doing it. There's some interesting anthropology hiding here.

      Have to say I'm a bit flattered that it's me that's being watched...

  7. Jul 2021
    1. Watched up to 2:33:00 https://youtu.be/wB89lJs5A3s?t=9181 with talk about research papers.

      Some interesting tidbits and some workflow tips thus far. Not too jargony, but beginners may need to look at some of his other videos or work to see how to better set up pieces. Definitely very thorough so far.

      He's got roughly the same framing for tags/links that I use, though I don't even get into the status pieces with emoji/tags as much as he does.

      I'm not a fan of some of his reliance on iframes where data can (and will) disappear in the future. For Twitter, he does screencaptures of things which can be annoying and take up a lot of storage. Not sure why he isn't using twitter embed functionality which will do blockquotes of tweets and capture the actual text so that it's searchable.

      Taking a short break from this and coming back to it later.

  8. Jun 2021
  9. Feb 2021
    1. Additional testing of pipeline portability is currently being conducted as a part of the Global Alliance for Genomics and Health (GA4GH) workflow portability challenge

      For more on how this went and an update on where the platform has developed to in Feb 2021 can be viewed in this video from CWLcon2021 https://youtu.be/vV4mmH5eN58

  10. Nov 2020
    1. As it becomes more clear what are specific functional jobs to be done, we see more specialized apps closely aligned with solving for that specific loop. And increasingly collaboration is built in natively to them. In fact, for many reasons collaboration being natively built into them may be one of the main driving forces behind the venture interest and success in these spaces.

      As it becomes more clear what the functional job to be done is, we see more specialized apps aligned with solving that specific loop. Collaboration is increasingly built natively into them.

  11. Jan 2020
  12. Nov 2019
    1. But in general the guideline is: code should be clean, history should be realistic.
    2. many organizations end up with messy workflows, or overly complex ones.
    3. If you push to a public branch you shouldn't rebase it since that makes it hard to follow what you're improving, what the test results were, and it breaks cherrypicking
  13. Feb 2018
  14. Apr 2016