All posts by Richard Gayle

Data transformation

potatoes by Avoir Chaud
Bioinformatics as mashup:
[Via business|bytes|genes|molecules]

bioinformatics: acquiring, collating and rearranging information already available elsewhere?

That is from a Tweet by Neil. My reaction was somthing along the lines of “boy that sounds like the definition of a mashup”.

Bioinformatics is a broad field, but part of it, a good part of what a bioinformatician does is exactly what Neil describes. The work of a bioinformatician is built on data collected by many people around the world and deposited in a variety of data bases. A lot of what we do is take information from one and try and match it up to information from a second source, presumably with the goal of getting additional insights. It might sound crude to call it that, but I think if we start thinking of bioinformatics as a mashup, we could start thinking about making those mashups available to others, and perhaps even new ways to present the information.

Disclaimer: This post was written early in the morning before any intake of caffeine

This is exactly right. Data just exists. It requires human interaction to provide context. Sitting in a database does nothing.

Mashups, as described here, take explicit information and transform it into knowledge. The key is to provide the right tools so that appropriate mashups can be performed. Perhaps Ubiquity will provide an avenue for such mashups.

Change the culture

coral by jurvetson
How academic health research centers can foster data sharing:
[Via Science Commons]

PLoS Medicine today published a new paper that provides useful guidelines for people at academic health centers seeking to support scientific data sharing. The paper, Towards a Data Sharing Culture: Recommendations for Leadership from Academic Health Centers, discusses both the enormous benefits and the obstacles to forging a research culture that fosters data sharing, and outlines practical steps people can take to set the process in motion.
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There are some very useful recommendations in the paper. It will really take some changes in scientific culture for some of them to be undertaken. But the faster these changes are made, the sooner the benefits can be seen.

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Ubiquity is hot

The ‘Ubiquitous’ web:
[Via business|bytes|genes|molecules]

MozillaImage via Wikipedia
All of you know about it already, but I shall happily add to the noise. Last evening I had one of those “Holy S**t” moments. Was sitting in a coffee shop, catching up with the days news, when I saw a flurry of activity on Friendfeed around Ubiquity. Turns out Ubiquity is a new project by Mozilla Labs, which for want of a better description is like Quicksilver for the browser, a mini command line available with an Alt-space.

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Ubiquity looks to be very interesting and useful. It will be nice to use this for various science mashups. One more reason to use Firefox.

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Blogging on research

sand by fdecomite
More on bloggers and OA:
[Via Open Access News]
Bora Zivkovic, ResearchBlogging.org, v.2.0, A Blog Around the Clock, August 29, 2008.

… [W]e took a little look [at the new release of ResearchBlogging.org] at the PLoS HQ and noticed that out of 87 pages of ‘all results’ there are 8 pages of ‘PLoS’ results – implying that about 10% of all the [ResearchBlogging.org] posts are on PLoS papers from all seven journals – and of those, 4 pages are just on PLOS ONE papers – which is about 5%. All I can say is w00t! for Open Access – when bloggers can read, bloggers will write.

ResearchBlogging demonstrates how blogging can be used to disburse information. The individual writers serve as excellent filters. It is like a journal club online, providing a way to cut through some of the jargon in a paper and see what its real relevance is.

It is one step above “Hey, did you see the paper in the latest Blood about X?” Now when an interesting paper is found, a short synopsis, with the proper attribution is available to a large network.

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Science blogging = new email?

 51 188520673 18F6208421 by cadmanof50s
Science blogging is the new email:
[Via Gobbledygook]

The just finished conference Science Blogging 2008: London was a wonderful chance for real-life socialising networking. I started to upload some fotos to Flickr (e.g. Scott Keir explaining sign language, see all fotos tagged sciblog here), some of them are too embarrassing and I will keep them for bribes reference later on.

The meeting was also a great opportunity to think about where we are today with scienceblogging. Having a conference is a good sign that the field is evolving1, and you can see several subdisciplines evolving:

  • conference blogging (also includes event blogging)
  • edublogging
  • metablogging (blogging about blogging, by far the largest discipline)
  • research blogging (blogging about scientific experiments, the smallest discipline)
  • investigational blogging (the keynote lecture by Ben Goldacre described this very well)
  • evolution blogging (a large subdiscipline)
  • news blogging (blogging about science news)
  • watercooler blogging (small pieces of interesting or funny thoughts/pictures)
  • summary blogging (summarizing other blog posts and linking to them)
  • diary blogging (blogging as a personal diary of self-expression)
  • hoax blogging (see this example by Jonathan Eisen)

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This is a pretty interesting framing of the use of blogs for research. A lot of useful scientific inquiry is informal in nature, occurring around a coffee machine or at a pub. Blogs just allow people who do not share the same time or place to participate. And in a more useful fashion than email.

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Loving FriendFeed

friends by freeparking
London Science Blogging Conference on Friendfeed:
[Via Confessions of a Science Librarian]

Boy, do I ever love Friendfeed.

You can follow what’s going on at today’s London Science Blogging Conference in its very own Friendfeed room. Each session has it’s own thread with multiple people commenting on the proceedings. It actually gives a very good and surprisingly understandable impression of what’s going on in the sessions. Most of the sessions have dozens of comments. Check it out.

You can also check me out on Friendfeed (join, you won’t regret it). Michael Nielsen has also created a room for the upcoming Science in the 21st Century conference.

As a sort of aggregator of one’s life, FriendFeed can be especially useful for all sorts of ad hoc social meetings, such as conferences. I wonder what the ‘room’ looks like for a really large conference, the 10,000 attending ones? I’ll be sure and check out the Science in the 21st Century room.

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The story of a teacher

Workflow- Social Media School Teacher:
[Via chrisbrogan.com]

classroom Dharmesh wakes up a little late. After a quick shower, he skips checking email, but goes right to his RSS reader to see updates of where the students worked within the social network. Luckily, Ning (and lots of services) send new activities out via RSS, so they’re easy to track.

It looks like Margarite has added more YouTube videos to the video section, and Franklin has written a blog post about the town’s historic water cooler. Jeremy has already commented that Franklin forgot to cite a source, saving Dharmesh the effort. He eats a breakfast bar, and hops in his car for the commute to work.

On his iPod, Dharmesh listens to last week’s book reports read out by the students. The quality of their work has improved a great deal since switching to the audio requirement. The second report, by Kelly, is a little loud and the audio clips a bit. Dharmesh makes a mental note to show Kelly how to level the audio in Audacity.

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Photo credit, LizMarie

These are pretty interesting representations of what the day might be like in a Web 2.0 world. Chris has a couple others – a minister and a marketer. They are nice ways to visualize the possibilities.

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Thoughts for discussion

pins by 416style
Beware of the Overload:
[Via Enterprise 2.0 Blog]
Information overload is a real problem as we develop new work processes to deal with it. At the moment, email takes the brunt, often serving as a catch basin for all types of data. This not only makes it inefficient, it makes it even more difficult to work through the large amounts of data that are usually included. Making the tools we already use more efficient in our workflow is critical.

Here we have a discussion of how one might do that. The Enterprise 2.0 blogs always has some interesting points.

Staying afloat in the depths of one’s email is a daily struggle for most of us. It’s difficult to carve out time to devote to other time consuming projects. Luckily there are collaborative tools that can help ease the strain. But just as important as the existence of the tools is the best practices associated with them. Here are a few I came up with:

1. A community can’t be force fed. It needs to take on an organic growth and naturally evolve. As a bottom-up movement, the members of the community shouldn’t need outside motivation to contribute. The benefits of membership should speak for themselves.

This is often true of a mature community and its tools. However, often the community needs some active gardening, particularly in the early stages, in order to become self-sufficient. This acts to increase the rate of diffusion of innovation for these tools.

While the benefits should speak for themselves, there is an element of internal marketing that often needs to be provided. IBM’s data indicate that corporate-wide initiatives have strong impacts on the creation and retention of new blogs. Care just must be taken to be sure that these sorts of top-down approaches do not hamper the bottom-up needs of the tools.

2. Be considerate of existing processes. Don’t anticipate replacing your email client with a wiki (just yet).

This is an important point. None of these new tools and processes will really replace another one. They will just provide a more appropriate avenue for dealing with large amounts of information. A screwdriver does not replace a hammer.

3. Know which tool is most appropriate for the task at hand, and use accordingly. Don’t try to fit a square peg in a round hole.

This is what is hampering email. Email is great for one-to-one communication where multiple forms of information (i.e. PDFs, photos, spreadsheets) can be moved between people. But is is not the best method for creating or distributing these to larger groups. Here, wikis serve a better purpose.

The goal is to make sure the tools are available. Too many communities only have round holes available. Thus the frustration.

4. Keep company policy top of mind when using tools. This policy should be communicated clearly. Removing a member’s post is justifiable, so long as the policy for what is appropriate content and what is not can be referenced as due cause.

Usually this only needs a light touch. If a company has done its job right, these sorts of policies will only be an extension of current corporate policy, such as appropriate emails. The community will fairly quickly determine what is really needed, particularly one that is already behind a firewall.

5. If you’re in management, be prepared to hear the truth – this may includes some things you don’t want to hear. A community is an excellent forum to spark debate and discuss issues business processes. It allows those in lower level positions the opportunity to have their voices heard.

This is a critical point. It is not that these tools create this voice. People already say these same things. The tools just make this discussion visible. Dealing with these truths will be an important skill to develop. The goal must be a more successful community and organization, not just to assign blame.

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A future position?

Workflow- Social Media for Marketers:
[Via chrisbrogan.com]

billboards What does a day in the life of a social media marketer look like? I’m not a marketer, so if I get some of your terms wrong, forgive me. I thought maybe we could do a walkthrough of a fictitious social media marketer, Yolanda, for a small hotel group (four hotels) in Boston. I picked hotels just because otherwise I’d have picked a software company. Let’s walk through a workflow, and then reconstruct it in bullets at the end.

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The rest is very interesting and provides a possible scenario for what the future might bring. Having people who are embedded in a community can be a tremendous asset for an organization. It sure sounds like a fun job.

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Technorati – still the best?

blog by Annie Mole
Technorati Doesnt Count Microblogs:
[Via chrisbrogan.com]

Something Mack Collier just said rang a bell in my head: Technorati doesn’t count services like Twitter, Friendfeed, Plurk, Identi.ca, etc, as valid sources of traffic for a blog. Meaning, for the dozens of people who say that they find something interesting and share the link on Twitter, none of that goes towards whether a blog is authoritative.

Does that actually make sense? If we’re shifting as a user base into using services like Facebook, Twitter, and Jaiku more frequently (okay, not Jaiku), why wouldn’t Technorati, the current reigning source of “authority” of blogs on the web, count these sources?

Has Technorati become the Alexa of measurement?

Update: I guess Alexa counts FireFox now, too. Again, if you have the bar installed. Thanks for the update. (Note: Alexa, as far as I know, only counts users of the IE browser with the Alexa toolbar installed in its ratings of who visits your website, versus Compete and others who count much more.)

Technorati is a great place to get numbers about blogs, or to learn about what is reverberating around the blogosphere. But Twitter, Friendfeed and others provide alternative means for blog-like information to move freely.

So, what is the premier site for analyzing blogs may find itself missing large swaths of data that essentially fill the same niche.

What should it do to adapt? Novel approaches for information flow will continue to be created and an organization can not continue to commit to a niche when the niche changes.

How does a group know when to take on new areas and when not to? This is one os the critical questions we face today. An innovation organization that is not ready to answer that question almost every day may not be around long.

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