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Housekeeping & Self References Semantics and Ontologies Standards

“Blogging is Hard” Day: Repost of 2006 FuGO Workshop Day 1

According to the rules set down by Greg Laden over at Science Blogs, I have had a trawl through the blasts from the pasts that was my 18 months or older blog posts to find one that is “exactly in lie [sic] with the writing or research in which they are currently engaged”. I thought about my Visiting With Enigma post, which has a special place in my heart, but didn’t choose it in the end as it didn’t have anything to do with my current research. Instead, I ended up choosing my very first post on WordPress: FuGO Workshop Day 1. It may not sound like much, but there are a number of things recommending this particular post.

  1. FuGO was the original name for the OBI project, of which I’m still a part and therefore it fits with the requirement that I still am involved.
  2. This was my first introduction to ontologies, and happened just as I was leaving one job (at the EBI) and starting a new one (at CISBAN). Such an important change deserves another mention.
  3. I notice an earlier incarnation of my “be sensible” statement in this post, where I say that I learned from Richard Scheuerman that it is always a good idea to use “only those fields which would be of most use to the biologist, rather than those that would make us bioinformaticians most happy”.
  4. FuGO wasn’t the only thing that has since undergone a name change. This post also contained information about the “new” MIcheck registry of minimal checklists: this has continued to gain in popularity, and is now MIBBI.
  5. Just last week at the CBO workshop, and again in a short discussion on FriendFeed that led to longer real-life conversations (Phillip Lord’s paper that deals with this topic), there was a long discussion at the FuGO workshop about Multiple versus Single inheritance in ontologies. This was also my first introduction to Robert Stevens and Barry Smith, who both took center stage in the MI/SI discussion. Listening to Barry and Robert speak was really informative and interesting and fun!

What a fantastic day that was: a crash course in ontology development and best-practices, as well as introductions to some of the most well-known people in the biological / biomedical ontology world. In many ways, those first few days of my current job / last few days of my old job shaped where I am now.

Read that entire post, and Happy Blogging is Hard Day! Thanks to Greg Laden for the great idea.

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Housekeeping & Self References

From WordPress to Vox and back again

From 2007 – April 2009 I have been posting on Vox, but have found it unacceptable for a number of reasons, and have come back to WordPress. Vox doesn’t allow proper analytics of the pages, and doesn’t allow proper trackbacks, and has problems with embedding any javascript or other code.

All posts from that time are still on Vox, but I won’t be adding any new posts there from now on. I used this tool to convert the RSS feed from Vox (which doesn’t include comments, unfortunately) into Moveable Type. From there, I could import the posts directly into wordpress. I know this means that the posts originally from Vox will be present in two locations, but I thought it best that my “active” blog contains an entire history. Some notes about the conversion process.

  1. Comments have not been copied.
  2. Tags are, by default, copied as Categories. However, the very useful “Category to Tags” converter within WordPress was very useful for this.

So, please visit me here rather than at Vox from now on – Thanks!

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Housekeeping & Self References

Seven Interesting Things

Well, I'm back after a month, and I thought I'd start out easy. I'd been tagged by Dan to try to figure out 7 interesting things about myself. I've never been a fan of chain letters, and while is a similar sort of thing, it was a friend who asked so I'm happy to oblige. However, I won't pass it on to 7 others 🙂 I'm also not a big fan of posting a lot of personal information about myself online, so I'm not going to stray too far in that direction. However, there are some family members I'm quite proud of, so that's the bulk of things.

  1. My maternal grandfather, George Oliver Atkinson Jr., was in the navy and was present during Operation Crossroads (1, 2, 3) on Bikini Atoll.


    He was part of the team that took the submarine USS Parche to the Atoll, where it became one of the targets of the blast. My Uncle sent me this picture he took of one of the letters my grandfather sent to my grandmother while he was en route – you can see the postmark is the name of the submarine. They sent sometimes 2-3 letters to each other every day, and numbered each envelope so when they were replying to each other they could reference each letter. Yes, these were nuclear tests that saw the residents of that area relocated, and nuclear explosions are not exactly all unicorns and rainbows. Irrespective of such thoughts, I am very proud that my grandfather was standing there, watching the explosions, and being involved in the process.

  2. On my Dad's side, my great-aunt (my paternal grandfather's sister) Marian Williams, was in showbiz. And she was glamorous! I don't have a picture, but my Dad has loads, and there are a variety of pictures online of the orchestra. My Dad can spot her in both Here Come the Co-Eds and When Johnny Comes Marching Home. (Here's a still from one of the movies.) In this picture, she's sitting with her saxophone over the shoulder of Phil Spitalny, vertically positioned between the accordionist and the trombonist, 2, 3). I'll try to get up a family picture. She was, among other things, a member of Phil Spitalny and His Hour of Charm Orchestra (1, 2) (I can't believe that I could find web pages that mention these family members!). This orchestra was an all-girl big band orchestra, and she played saxophone, clarinet, among others. I still have a tape kicking around of a record that my Dad has of the orchestra.
  3. I've recently discovered that I'm a third-generation programmer! The same grandfather that was involved in Operation Crossroads worked on some interesting programs in his later days in the Navy. As my Uncle says, "just before he retired at the height of the Cold
    War, Dad worked with the Joint War Games Agency section for the Joint Chiefs of
    Staff.  He designed and programmed the first computer War Games Modeling
    software, written in machine language and punched onto tape.  So I never
    knew, when I chose programming as a profession, that I was following in Dad's
    footsteps until around 1985, when the stuff he worked on was declassified and he
    showed me some of his design documents." That was the first generation, the second is both my Uncle and my Dad, the latter of whom in the course of his postgraduate studies used punch cards to program the SAS statistics software.
  4. I don't like coffee. That's why they kicked me out of the USA.
  5. I enjoy geocaching.
  6. When I was very small (toddler or just a bit older), my family found me sitting on the dining room table eating a stick of butter. Yum!
  7. I enjoy knitting and crochet. Included is a shot of my current work 🙂

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Title Change Revisited

Trying out another name (see title of blog above): this time it's "The Mind Wobbles" (see my previous post for the history behind choosing a title). The mind wobbles is the name of my (mainly defunct) wordpress site, so it would make sense to use the same name on my Vox site. Additionally, it has a nice ring to it (and Deepak seems to agree!) It would mean the name would be catchy, but not directly related to my work, which would allow me to change work area and not have to feel the blog title no longer fits.

I'm trying it out now in parentheses in my blog title, to see how I like it. I originally chose it because of the Weebles (weebles wobble but they won't fall down). I like my puns, and thought this was punny. Anyway, comments, as always, welcome. 🙂

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Title change?

I’m horrible with title creation: I can never think of a good title for papers, projects, etc. Any sort of naming just causes me problems, hence the completely boring name of this blog (Systems Biology & Bioinformatics). But I’ve been trying to think of a good, more permanent, blog name, and I think I’ve found one. However, I’m quite nervous that, even after my google search, I may find out that this was a horrible name after all, so I’ve gone quite tentative and am currently road-testing the new name by putting parentheses around it. The new name could be “Semantically Speaking”, and I’d like to know what others think. It won’t change how I post, just the main name. I’ll retain the SBB part in the sub-title, together with the keywords already present. There is already one blog with this name, but it’s two years since the owner’s made a post, and it isn’t in the same topic area. The other google results are mainly about individual articles, and not websites of the same name.

So, here’s your chance – would you like to help name a blog? Do you agree/disagree that this is a good name? I need your help! 🙂

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Housekeeping & Self References Semantics and Ontologies Standards

This site now listed in Nature Blogs, and the reason behind my keyword choices

Last week when scanning through Friendfeed, someone mentioned Nature Blogs. A number of my friends and fellow friendfeeders (1,2,3,4,5,6,etc.) already have their blogs registered there. I took the plunge and submitted my request last week, and this site was accepted for inclusion in the list this week. You can find it listed under the bioinformatics category. In honor of that occasion, I've decided to post a summary of the tags I chose to mark this blog with on Nature Blogs, and the reasons for them. (The obvious one, bioinformatics, wasn't necessary as far as I could tell because that is the top-level category I've placed the site into.)

  • data integration: It is the main focus of my research, and one of the biggest challenges facing bioinformatics and the life sciences in general. So many formats, so little time! Reconciling these using brute force, standardization, semantics, and sneakiness are what it's all about.
  • ontologies: I like ontologies for many reasons, not the least their potential for reconciling the many different ways of defining and naming things in our lives. We need a common ground from which to perform successful integration and analysis, and I think a well-written ontology (or set of them) is a beautiful thing. They are a major tool in my research bag of tricks. Not only that, but I also help develop a community-driven ontology for describing life-science experiments (OBI).
  • workshops: my method of remembering what goes on in workshops and conferences is to take notes, and I can be a pretty fast typist. I enjoy blogging on each lecture at such an event as they happen, and you'll notice a lot of workshop and conference posts on this site. They are mainly written while the speaker is speaking, with a minimum (if any) of later editing. However, if any speaker reads my notes and would like to suggest areas where I made a mistake, I am more than happy to make those sorts of changes. One of my favorite ways of blogging.
  • systems biology: that's the field in which my bioinformatics research is applied, which makes it an immediately-applicable tag for this blog. But try to define it and, as with so many things in this world, you could get as many definitions as there are people. (Ok, perhaps a slight exaggeration for dramatic effect.) So, I'll not try to define it today, and just say that my posts often deal with work in this field.
  • science outreach: My Mom is a teacher, my Dad was a teacher and remains working in Education. If it wasn't so much hard work, I'd consider it as a career myself. 🙂 However, I do enjoy trying to pass on my enjoyment of and interest in the sciences. Some of my more recent posts talk about the work I'm doing with the Teacher Scientist Network. Outreach is just fantastic, especially when explaining science to kids, and it's something I like to talk about in this site, when the opportunity arises.
  • standards: Perhaps it's because I spent years working at the EBI, where they provide databases and services in specific syntaxes. Perhaps it's just the way my personality is. Whatever the reason, I really enjoy working with data standards. I'm lucky enough to be directly involved with two at the moment (FuGE and OBI), and peripherally involved in other efforts such as SBO (by peripherally I mean that I've nagged them in the past about the whys and wheretofores of various aspects of their ontology) and MIGS (I was involved in the initial work on the checklist, and provided advice on FuGE). I'm a bit of a standards fiend, and try to remind myself that not everyone finds them as interesting (though everyone should at least find them relevant!).

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The excitement of being mentioned in a podcast

Another first for me – one of my posts has been mentioned in a podcast! It made me grin – it was a lovely surprise!

My thanks go out to Deepak and Hari on the Coast to Coast podcast as well as Chris Lasher: the former two guys for mentioning my blog post about my day talking to kids at a local school in their 4th installment of their podcast, and the latter for letting the C2C pair know about it via delicious links (you can add to the C2C bookmarks by adding the for:c2cbio tag, as you can see in the Coast to Coast Podcast's Delicious page). In fact, Hari mentioned that the post was quite timely for him, as it helped him in making his slides for a school in Massachusetts: I'm glad that my experience helped you out! Deepak also mentioned that he wanted to try to talk to high schoolers (before they get into the university "publish or perish" system) to educate them on the growing importance of "Big Data" management, and social networks in the sciences as additions to the traditional publishing routes. I think that's a fantastic idea.

This 4th installment covers a lot of other interesting topics, including the Galaxy Zoo, more information on science outreach, how Mathematica has changed, and the importance of Linux. I've also just listened to the 5th installment, where they talk about how iTunes is noticing an increase in listeners (I don't listen via iTunes – does my download count for you guys somewhere? 🙂 ), how web services and the Embrace project are good things, and detail some of the things going on with the Elsevier grand challenge. Enjoy!

(P.S. A final thanks to Dan over at Eridanus for the head's up: I had only made it through the first couple C2C podcasts – without the IM with him this morning, it would probably been another week before I managed to catch up. Vacation is great, but sometimes it means you come back to a lot of backlog!)

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