MicrobiologyBytes

So you’ve heard about Flipboard, the publishing sensation on iPads? I’m a huge fan and I’ve been writing about Flipboard on my other blog. But you don’t have an iPad? I can help you with that:

MicrobiologyBytes on Surfboard

Ride the wave!

Last month Martin Fenner wrote about creating a reading list for his blog, Goobledygook. This was such a good idea that I decided to copy it, so now you can get a list of all the papers referred to on MicrobiologyBytes. (It doesn’t go all the way back to the beginning of time, but I will keep it up to date from now on.) Of course, you might already have your own system for filing away the references from this site, but if not, I’m making them available to you in a handy and easy to access format (if you’re not familiar with CiteULike (or Mendeley) it’s worth checking them out):

CiteULike (RSS feed)

So how might you use this? Well that’s really up to you. Whether you’re a teacher preparing a lecture or a student writing an essay, you may vaguely remember you read something about it here, you can search through this site or search through one of the reference lists, which will provide you with the full reference in a format you can insert directly in your writing.

I’m sure there will be lots of other ways this will be useful to you. Please let everyone know what they are by leaving a comment below.

I’ve been very busy over the last few weeks, mostly going to and talking at a whole series of conferences, but also not writing Principles of Molecular Virology (too busy), and spending lots of time sitting in hospitals waiting to get my antibiotic fix for an annoying eye infection. As a result, MicrobiologyBytes has been a bit lightweight recently, and I apologize.

But now it’s time to get going again! I really appreciated the feedback from everyone who contributed to yesterday’s post, and I’ve got a few good ideas I’d like to try out over the next few weeks – make sure you tell me what you think of them when I roll them out. Most importantly, from tomorrow, we’ll be back on a regular schedule with all the microbiology you can take! Stick around and keep commenting :-)

Thanks to everyone who left a comment on yesterday’s post. If you’d like to contribute, there’s still time, and I don’t mind if you prefer to remain anonymous.

Tomorrow, we’ll get back to some microbiology :-)

Every day several thousand people read content from Microbiologybytes, either via the website, RSS subscriptions, Friendfeed or Facebook. And that’s great – I’m really pleased people find it so useful. I’d like to make it even better, but I can’t do that without your help. I’d like you to tell me what you find most useful about MicrobiologyBytes, and how it can be improved. I’m particularly interested in:

• Who are you and what’s your background – student, teacher or interested passer by?
• How long have you been reading MicrobiologyBytes?
• How often do you read MicrobiologyBytes?
• Where do you read MicrobiologyBytes – website, RSS, Facebook?
• What do you like best about MicrobiologyBytes?
• How could I make MicrobiologyBytes better for you?

If you like to let others know who you are and what you think of this site, please leave a comment below, and if you want to leave your name. I’ll get back to you.

Thanks :-)

Most of my work over the last few years has been involved with science education, and much of the online effort has gone into surfacing aspects of the scientific literature by making it accessible to a student audience, and indeed the general public, should they be interested. Mostly, this has meant developing the MicrobiologyBytes website, along with its Twitter, Friendfeed and Facebook satellites. In my “education hat on” guise, I write frequently online about my work on Science of the Invisible, Twitter and Friendfeed. So why would I need another public outlet?

Open notebook science (ONS) is the practice of making the primary record of a research project publicly available online as it is generated. This involves placing the personal, or laboratory, notebook of the researcher(s) online along with all raw and processed data, and any associated material. The approach can be summed up by the slogan “no insider information”. This is far from the norm of scientific practice, but over the last year of talking to some of the leading practitioners of ONS, notably Jean-Claude Bradley and Cameron Neylon, I have become convinced that I would like to try it. One part of our feasibility test is a new blog, a space where our part-formed thoughts, ideas, planning, and general commentary on ONS stuff will appear. The other part is our open notebook on Wikispaces, where all the data will be posted. If you want to follow our progress, subscribe to the RSS feed for this blog, or go to this page and subscribe with the feed reader of your choice. If you prefer, you can receive updates via your email account.

Open or closed? It’s not that simple. There are many flavours of ONS, and it’s not clear yet which one(s) we want or are able to pursue. Indeed, our style of “open” is one of the first things we need to work out about this project. For a variety of reasons, not all of the research done in our laboratory will switch to ONS. Initially, we intend to try it out with a new project we are developing (which is described below). Thus our approach to ONS is itself an experiment. Only time will tell if we are able or willing to continue in this format. Apart from funding, it depends whether this idea wins hearts and minds – not only in our lab, but beyond it. In part, that depends how much interaction we receive. the project we are beginning is a new field for us, so we don’t expect the world to be queuing up to help us, but to be successful, the downside risk of ONS needs to be balanced by the upside of helpful positive interactions from interested observers.

So what about the science?

The chytrid fungus Batrachochytrium dendrobatidis (Bd) is an emerging pathogen of amphibians worldwide. The aquatic zoospores of this primitive fungus infect larval or adult amphibians, and, depending on the host species and other factors as yet unknown, may cause anything from 0-100% mortality. Coupled with climate change, pollution and habitat loss, chytridiomycosis (or “chytrid”, pronounced “kit-rid”) is a serious threat to many amphibian species. Bd research has moved from obscurity to prominence very rapidly over the past few years, and two complete genome sequences are available (JAM81, JEL423):

http://dan.corlan.net/medline-trend.html

So where do we fit in?

We are trying to leverage our existing skills in molecular biology, antibody production, protein chemistry and microbiology to study this organism. In part, this is because of an interest in the environmental impact of this emerging pathogen, but we are also interested in studying Bd as a model organism to examine aspects of fungal biology and pathogenesis. We are currently interested in developing work in the following areas:

MicrobiologyBytes is designed to give you the latest news about microbiology, but how you consume the information is up to you. You can visit the microbiologybytes.com website, subscribe to our RSS feed, tune in via Twitter, or if you want to, you can get MicrobiologyBytes on Facebook:

It’s free, and it’s your choice :-)

Today I’m going to be at Science Online London (programme). I wasn’t able to attend in person last year, but I followed the live streams online and gained a lot from it. You can follow @soloconf on Twitter, hashtag #solo09, but judging from last year, most of the action will be in the Solo09 FriendFeed Room:

The Web is rapidly changing the communication, practice and culture of science. Science online London 2009 will explore the latest trends in science online. How is the Web affecting the work of researchers, science communicators, journalists, librarians, educators, students? What can you do to make the best use of the growing number of online tools? This is the follow-up conference to last year’s Science Blogging 2008: Londonconference. The name of the event was changed to reflect the variety of science-related activities happening online today. Topics include blogging and microblogging, online communities, open access and open data, new teaching and research tools, author identifiers and measuring the impact of research.

See you there, or see you online.

“More researchers should engage with the blogosphere”

The blogosphere differs from mass media and specialized media in many respects, but the same considerations apply in disseminating new scientific results there. Authors of papers in press have the right to correct misrepresentations and to point to results that will appear in a paper. But a full discussion should await the paper’s publication.
Indeed, researchers would do well to blog more than they do. The experience of journals such as Cell and PLoS ONE, which allow people to comment on papers online, suggests that researchers are very reluctant to engage in such forums. But the blogosphere tends to be less inhibited, and technical discussions there seem likely to increase.
Moreover, there are societal debates that have much to gain from the uncensored voices of researchers. A good blogging website consumes much of the spare time of the one or several fully committed scientists that write and moderate it. But it can make a difference to the quality and integrity of public discussion.

Nature 457, 1058 (26 February 2009)