Reloaded…Again…Again, or Memories of ISMBs Past

Who out there remembers ISMB 2009? If, like me, you need a refresher then take a look at the ISMB 2009 Summary and Highlights article that I wrote at the end of it. We all enjoyed Sweden, and had a lot of fun. Due to an increase in my family size by two over the intervening years, and a concomitant switch to part-time work, I haven’t been back to an ISMB since. Shocking, I know! I love conferences, and hope to start going again soon, but until then, take a good long look at my badge-based blast from the past, pictured on the right.

Were you carbon based or silicon based? Do you still have your badge? Please let me know!
Were you carbon based or silicon based? Do you still have your badge? Please let me know!

Now, I’m pretty sure that this badge came from the conference party at ISMB 2009. Please can someone confirm this though, as clearly 2009 is a Very Long Time Ago.

…Anyway, at least I remember the party! As we came in, we were each given a pair of sunglasses and had to choose a badge. Carbon-based badges were for people who had studied the life sciences before they came to bioinformatics, and silicon-based badges were for those with a Computing Science background. I chose carbon based as my undergraduate work was in Biology, although all subsequent study was in bioinformatics.

Anyone remember ISMB 2009 and have any experiences they’d like to share, especially with regards to this badge? Were there better parties at other conferences? I’m pretty sure Tainted Love came up at one point while a large proportion of the delegates were dancing. But then, I may be confusing my conferences. Hmmm, must take notes on more than just the lectures next time!

When three scientists walk into a primary school…

Last week I had another volunteer session as a STEM Ambassador with a local primary school. I was one of three STEM Ambassadors (as well as the lovely STEM coordinator Catherine Brophy) who spoke for an hour with a variety of Key Stage 2 children (anywhere from around 7-10 years old I think) about being a scientist. They interviewed all four of us about what it means to be a scientist, why it is fun/important, and more. When I wanted to speak a bit more about what it means to “do biology with a computer”, I referred occasionally to these slides I had made for a similar purpose a few years back:

The slides are full of pretty pictures (the notes to accompany these slides are also available on my blog) and they gave me a way to focus the children’s attention. However, the kids last week really didn’t need much focusing, and asked lots of great questions. They asked if I had invented anything (does inventing biological data standards count? I think so…!), who my inspirations were (my high school Biology teacher of course, among others), if I had any pets (slightly off topic!), and what my greatest accomplishment was (my thesis – phew!). They all seemed really animated, which is one of the best perks of going to a primary rather than a secondary school. I love the fact that secondary school students can handle more complex discussions, but the enthusiasm of primary school kids is just stupendous.

This trip to a primary school was very timely, as I had recently been to a parents’ meeting at my own son’s primary school about the change in the English school system away from levels. The head teacher was fantastic at explaining the changes, but one of the things I noticed about the new system was a seeming lack of guidance for schools in the science curriculum. It worries me that primary schools are being edged away from teaching science due to a large emphasis on English and Mathematics.

However, this is an issue that the STEM network can help solve. As ambassadors, we can come into your school and talk about science, how we became scientists, and why we love it. Last week it was three scientists talking, but the STEM network can provide experiments and other visual aids too, as well as helping schools enter science contests and fairs such as the Big Bang.

We had fun last week. We had a chemist (with a background in maths) who brought props: a cow bone, jelly babies, hair dye and other things. She asked the kids what the cow bone and jelly babies had in common (gelatin!), and quite a few of them knew. The other biologist had done field work with butterflies, and had the children imagine how you could mark or safely trap them. I talked about the structure of DNA (one child knew the comparison with a spiral staircase!), and how science was great because you don’t have to accept what anyone says “just because”. You don’t believe them? Test it! Science is imagination, testing, and reproducibility.

You don’t have to take my word for it “just because” I say it’s great – become a STEM Ambassador yourself, and test my statement that it is a completely awesome thing to do 🙂

Back into data standards with BioSharing

biosharing-logoBy the end of last year, I had finished my work with both Manchester and Newcastle. Happily, I’ve found a new (working) home with Susanna, Philippe and the gang at the OERC in Oxford. I’ll be working part time on the BioSharing.org project, and will be doing all sorts of things related to biological data standards, policies, and databases.

I have a history in biological data standards and in developing community-driven standard formats, checklists and ontologies. I look forward to devoting some time to this collaborative, integrative project, and to helping people structure and manage their data well. To finish, here is a little bit about BioSharing, taken from the website itself:

“BioSharing works to map the landscape of community developed standards in the life sciences, broadly covering biological, natural and biomedical sciences. […] As part of the growing movement for reproducible research, a growing number of community-driven standardization efforts are working to make data along with the experimental details available in a standardized manner. BioSharing works to serve those seeking information on the existing standards, identify areas where duplications or gaps in coverage exist and promote harmonization to stop wasteful reinvention, and developing criteria to be used in evaluating standards for adoption.”

Image from http://www.biosharing.org/pages/about/
Image from http://www.biosharing.org/pages/about/

A Pause in Posting

You may have noticed a pause in my posts (here, and on Twitter, and on G+ etc. etc.) – this is due to an 8 lb 15 1/2 ounce (4.07 kg) bouncing baby boy coming into our lives this past July 🙂 So my apologies, I do plan to post more about bioinformatics and ontologies in the near future, but as this is a work blog (and not a baby blog!) there will be a little break now. Normal service will resume, eventually!

The reason I'm not posting to this blog at the moment :)
The reason I’m not posting to this blog at the moment 🙂

PhD Thesis: Table of Contents

Below you can find a complete table of contents for all thesis-related posts (you can also get to the posts via the “thesis” tag I have used for each). Enjoy!

Thesis Posts

And, if you’re interested in how I performed the conversion, I’ve written about that too.

A new journal, a new bogus review: again, the culprits are banned

This is an update on an earlier post, A case of stolen professional identity, which is just a little too long to add directly to the original post.

Last month I received a request for review. But it wasn’t just any request: the title looked suspiciously similar to the title of a paper whose review I had been asked to confirm back in March. In the original incident (described here), the culprits were found to have created a false gmail account for me and submitted my name as a reviewer with that false email account. They were banned from that journal (let’s call it Journal1). I really didn’t think they would try again, at least not with the same fake review setup (specifically, my name and a false email account).

But they did.

Journal2 sent me a standard review request in June. It turns out that behind the scenes, a bogus email address was used, though I’m not sure it was the same one used for Journal1. The affiliation that was provided to Editor2 by the author of the submission appeared strange to him, and so Editor2 searched for me online and found my institutional address. And, as with last time, mine wasn’t the only identity used fraudulently. I noticed the similarities, and I put Editor1 in touch with Editor2, they compared notes, and discovered it was the same paper, the same authors, and the same trick being attempted again.

Turns out fake emails weren’t the only fake thing about them. Though I don’t know the details, I believe there were also fake phone numbers and perhaps fake affiliations.

The authors have been formally banned from Journal2 (as happened with Journal1), and I have to say I wanted to cheer when I saw the words “Please note that this type of behavior is not acceptable in science and will not be tolerated.” Editor2 is going to move things forward, including bringing it to the attention of the Committee on Publication Ethics. I am also looking into ways to take away the false gmail account from whoever owns it, so that hopefully at least that permutation of my name cannot be used again. However, that isn’t a practical solution in the long term, as there are many, many possible permutations.

I had hoped it wouldn’t happen again, but it has, and quickly. Seems like the single thing that would help the most, while needing the smallest change to the existing system, would be to require institutional addresses. Additionally, open peer review might help, though you’d have to do a regular search to ensure that someone didn’t publish an open peer review pretending to be you. My thanks go to both Editor1 and Editor2 for allowing me to, once again, write about these experiences. With knowledge comes great responsibility, yes, but also forewarning.

And I hope it doesn’t happen again. Again.

How can socks facilitate scientific outreach?

OK, it seems odd, at least on the surface. How can socks help science generally, and science outreach specifically? I asked myself the same question a few months ago when I found an email lurking in my inbox, hidden since just before my maternity leave started. It seems a sock company called Sock It To Me socks featured a different Cool Girl each month, and they wished to feature me. I had a lot of questions. Was this for real? Was it an appropriate platform to be talking about myself, and about what I do? Would it seem as if I was trading my online work persona for socks?

Well, the other Cool Girls’ profiles seemed eclectic and interesting: dancers, astrophysicists, mathematicians and many others. So, not bad company to be in, and it was a genuine request. And, before you ask, I will be getting two pairs of socks for my efforts – ah, temptation. But ultimately, I need to take care of my work/public online persona, and I had to decide whether this was a good addition. But then I realized I could talk about ontologies to people who may have never even heard of bioinformatics and, for me, that was too exciting an opportunity to miss. True, it was limited to 600 words, and a writer used the information I gave her to write the final piece, but I think it was all worth it. She did a great job, and within the confines of the article format, I’m happy about how my field of research is portrayed. I really feel strongly about science outreach, and I do think that novel methods of information dissemination shouldn’t necessarily be ruled out.

So, here it is: Ms Cool Girl of the Month, July 2011. What do you think? Did I benefit science or just myself (well, maybe not just myself – I namechecked my high school biology teacher, and mentioned Cameron too)?