Bioinformatics Zen

Pigs are clever animals, and certain people of the right persuasion might find them cute. Realising the market potential of pet pigs, I spent a couple of years selectively breeding them until they were around the size of a household cat. The iPig is small, cute, and just as clever as a normal pig. Combining a great product and some investment capital I started a business based on the iPig. The iPig is a new and novel idea, so I needed to persuade a pet store of the selling potential of the iPig. This was not easy as some pet stores are sceptical about new types of pets, but on the condition I make some changes to the marketing, the iPig was accepted at a chain of pet stores. So I’ve bred the iPig, and got it accepted at a local pet store, I can relax and think about the next product in the pipeline.

Why stop there? The iPig will continue to sell as the pet store gets a steady stream of customers, but I’ve been thinking recently though, I’ve spent a huge amount of time breeding up the iPig, could I also do a little bit of marketing to maybe boost sales of the iPig? Doing a bit of work on the web would be a small effort compared to the amount of work I’ve put in already. So I create a short video explaining what I think is great about the iPig, I also start a wiki to help other users in the development and care of iPigs. Neither of these take much work, and easily findable on the web via keyword searches. Many businesses uses web tools such as blogs and twitter to engage with customers, so in future I might also consider doing something like this for my company. Even further, I know other people are able to create a business model from open sourcing their development process, so I could test how this is useful for the development of the iChicken.

I’m going to return to reality now for a short exposition of the point I’m trying to make. Can you treat your research as a product you believe is important and that you want the rest of the scientific community to know about? For example in future it may that, a research department’s output will be increasingly measured on the number of citations published articles receive. Getting work published in high impact journals won’t go out of fashion any time soon, but the increasing growth of science on the web gives you and your department the tools and ability to increase the number of people who see your research, and therefore include that research in the development of their own work.

Pictures: beeldenzeggenmeer and liberodicrederci

The title says it all. I was hoping to release this a month ago, but standardising the survey data was a bigger effort than I anticipated. Finally though, you can download the results in CSV format from Github. If you don’t know what CSV format is, don’t worry as the file should open in Excel, OpenOffice.org, or any spread sheet application you care to point at it. The only other thing you need to know is this data is released under a Creative Commons Attribution, Share-a-like, Non-commercial license, if you need to know what this licensing means you can read the full explanation.

That’s it in a nutshell, the details about sharing and posting results can be found on Open Wet Ware, including some example analyses I’ve posted.

July is over, and therefore so is the period for collecting results for this career survey. In total there are 681 entries. The top ten list of countries for results is shown in the graph below. The most entries were received from the USA, almost double of those received from France in second place.

World wide, the survey received entries from 52 different countries, which last week included Uganda, Nigeria, Zambia, Tanzania, Iran, and Saudi Arabia. The distribution of countries in the survey is shown in the map below.

Finally I organised the results by macro-regions which, as you might expect, illustrated that the majority of entries came from North America and Europe.

Releasing the data

The next step is to release the data under a creative commons license, so that anyone who wants to, can analyse it. However, at the moment I’m just going through the data to tidy it up, such as converting converting figures like $30k to 30000 so that the results are standardised, and programmatically readable.

I had been thinking about a creative commons share-alike license, so that any derivative results are also released in the public domain. I had also thought to host the data, as well as create a page for collaboration on Open Wet Ware. All suggestions towards this are really, really welcome though, as the plan for this isn’t fixed, and there is a large element of working things out as they go on.

Another great week for the survey, where the total number of entries now exceeds 600. Thank you to everyone who has filled in the survey, or posted a link on their website. Special thanks this week to everyone on friendfeed who volunteered to forward the survey on a bioinformatics related mailing list, and to everyone who spread the word at ISMB. This is the last week of July so on Friday, I’m going to press the stop button, and release the dataset for everyone interested to start producing lovely plots and graphs.

As for current status of the results you can see France has leaped up to second place in the number of entries received, which may be something to do with Pierre forwarding the survey onto a French Bioinformatics mailing list. Furthermore Switzerland is a surprise new entry at number 9, edging Italy out the top 10.

As for geographic disribution of results, the map shows there is now at least one entry from a large proportion of the world. Specific new entries this week were from China, Russia, Finland, Jordan, and Cambodia. I think it would be great to have more entries from Africa before the end, as the continent is only represented by two countries: Kenya and South Africa.

There are five days left, and I think it would be great to have 800 entries before the end. If you’re reading this blog, I would guess that you’ve probably already filled in the form, so instead of asking you again to fill in the form, I’m asking if any one has any suggestions for a final burst of publicity. The survey has already been forwarded on to a variety of bioinformatics mailing lists, but if you know of one that hasn’t been contacted and you think that may be interested, that would great if you could send an email about the survey. Any other suggestions for publicity are welcome too.

The original post, for the Bioinformatics Career Survey

As you are reading this, the number of entries for the bioinformatics career survey should have just reached 400. With two weeks passed, and two more weeks to go, the survey is halfway through. If you haven’t already filled it in, please try and take a few minutes to do so, you can leave any fields blank that you’re uncomfortable with.

As for the results, in the second week USA and Spain are still first and second place respectively. The UK has moved up to third to overtake Germany in fourth. Possibly related to a link on the Nature India Blog India has taken fifth place, with Australia now in sixth. The remaining positions remain the same as the previous week. There is only a two point difference between the UK in third, and India in fifth, while only four entries between France in seventh and Italy in tenth, so a few more results from any of these countries can easily change the order.

I used IBM’s Many Eyes website to visualise the results by region, as it allows you to interact by zooming in, and roll over countries with the mouse to get results . From the map the results are mainly centred on North America, Europe, and the India/Australasia regions, but it’s interesting to see a couple of entries from Kenya and South Africa, as well as Columbia, Brazil, Chile and Argentina in South America.