Nature Protocols likes to be part of the on-line community. In addition to the main journal (which, in 2006, was one the first NPG titles to have commenting on its articles), we have the Protocol Exchange, Stepwise (the blog), a twitter account and – the subject of today’s story – the Nature Protocols Discussion Forum.
The Discussion Forum was set up to create a place where people could post questions about methodological problems encountered in their research or discuss various methods and techniques. Dot is the main person looking after the forum, so it is slightly unusual (and a little exciting) for me to take part of any of the discussions. Browsing through the topics, I found that broadly speaking there are two types of questions that seemed to come up frequently on the forum:
(1) I am thinking of doing this experiment, does any one have a good protocol or some advice on how I should go about it (e.g. trying to generate a site specific acetylation antibody)?
(2) I have done this experiment, and it all went horribly wrong, does anyone know why? (e.g. Galactose induction of Yeast cells)
About a week ago, a researcher emailed protocol.exchange<at>nature.com with some Type 1 queries regarding the electrophoresis of DNA and I helped him by posting a topic on the forum.
We alerted our twitter followers to the cause…
…. and three very helpful researchers replied.
While it is possible that we might have reached the “happily ever after” state for this forum topic, “Should I use agarose or polyacrylamide?” and “How long should the gel be?” may actually have the kind of answers that starts “It depends…”.
If you have any thoughts on the subject, or know of a good open access resource that discusses any “It depends…” aspects of the DNA electrophoresis question please do join the discussion!!