Tips and Tricks - Where next?
June 13th, 2007The recent release of the bio::blogs “tips & tricks” special has proved popular and comments from three readers suggested continuing it further. But I’d like to know what kind of interest there would be in this. And how to carry it out.
One possibility is to aim for regular release cycles, for example every 4/6 months. Each issue would be on a specific topic, such as sequence analysis, network analysis, etc. This could be co-ordinated and set up on a wiki site.
Another idea I had is to set up a semantic wiki, the aim to create both a human and machine readable resource. This would be particularly useful for categorising the tools and databases available in bioinformatics.
These are just two examples, but I be really interested to hear your suggestions. Posting an idea here isn’t a commitment, it could just be something you’d like to see. Like most amateur web ideas, it would probably just be me initially, and if it was useful, other people would naturally become interested in helping.
Of course the other suggestion is that this is just a successful one of a kind that should be left so.
June 13th, 2007 at 10:37 pm
I would definitely like to see the continuation of tips and tricks. One factor to consider is how much time/effort you are able to devote to it. These things can easily get out of hand
I like the wiki idea - there’s a gap in the market for a “web cookbook” of bioinformatics. It needn’t be just code or programming how-tos, some of the best tips in the first edition focused on issues like productivity, collaboration and work habits. Practical advice and examples would avoid overlap with wikiomics, which is more of a general information site from what I can see.
Having articles stored in a wiki would also make it easy to pull out a selection for a compendium every few months - most wiki software has an export to PDF plugin, for example.
June 13th, 2007 at 11:03 pm
Hi Neil, thanks for your fast response.
I agree that running a blog and a wiki could become a lot of work for me. I’d also thought about wikiomics too, and overlapping with that would be counter productive. It would need a goal - something clear and separate from wikiomics.
When I conceived this website, it was to focus on all the things that get ‘missed’ in traditional bioinformatics training. Here’s an example, when I studied for my masters I learnt a lot of useful things about computation, statistics and biology. But one of the hardest things you don’t really get taught is the ethos of being a bioinformatician, or computational biologist. Discipline, time management, phrasing dry work questions. I know that sounds wishy-washy, and it is a bit, but hopefully you get my point. There is something in the gaps and spaces that take you from being a somebody who uses computers in biology, like a wet lab scientist, to really getting to important questions and answers as the next logical scientific step from producing data in the lab.
That’s what I hoped I get from starting this blog. Going from being handy at creating code and running statistics, to asking the right biological questions and producing relevent answers. Without checking my email too often everyday, of course.
June 14th, 2007 at 11:18 am
Mike,
re: databases. You might want to look at
http://biodatabase.org/index.php/Main_Page
I have tried to nudge them down the semantic wiki path, but I don’t think it’s going to happen, and quite frankly for something like this I think it’s essential. As far as tools goes we used to mark them up using an EMBOSS style designation for filing when I was developing Bio-Linux at NEBC. Which might be a starting point for something like this.
I do like the idea of focused ‘tips and tricks’ articles every few months like the Bio::Blogs one. I’ve just had a request to include the article I wrote for http://scitizen.com, which was nice.
June 14th, 2007 at 12:37 pm
I totally agree Mike and that is why these ‘Tips & Tricks’ are so useful for Bioinformaticians regardless of experience. I suppose its out of the scope of any masters course to teach you all these things and you have to rely on your own initiative and self development.
You are taught a lot of skills and techniques intensively and have no real time to ponder on interesting questions that these could answer. For this reason I feel that the majority of what I learnt from the course was during the final project where we were able to consolidate and augment our skills and experiences further and channel this into a specific direction with real goals.
June 14th, 2007 at 1:55 pm
Thanks for your suggestions about semantic wikis. If you’ve got a moment take a look at Makna and COW, it’s easy to imagine how these could be applied to the organisation of bioinformatics tools and databases. The problems in this would be creating the vocabulary that everyone would be happy with, as well as the effort involved in initially filling it with data.
As for the tips & tricks edition, I had think about it overnight. I thought an interesting topic for the second edition would be open science. It’s something that’s starting to garner more interest from both researchers and journals, also it’s a topic that’s not very clear. So an article on this could be useful, especially if we could get contributions from journals on their stance. Perhaps aim for an October release with Bio::Blogs, if Pedro thinks it’s okay?
June 15th, 2007 at 11:07 am
I am all up for new ideas :). As far as I see Bio::Blogs is for/from the community. I really liked the Tips & Tricks both because of the amount of participation and nice design.
It would be nice like Neil said if there was some easier storing and maybe a way of handling the production pipeline. For the PDF output I never really used LaTeX but I might have a look a it. For the storing of information even the Nodalpoint Wiki could do.
Open Science is a nice topic. I am not sure that we can get comments from journals but we can try. Nature at least has been putting out editorials of sharing data etc so they might just fall back on those statements. From other publishers we might just get fuzzy PR speak.
We could work on a couple of questions to ask editors/publishers/scientists/bloggers.
June 15th, 2007 at 2:32 pm
Thanks for the positive feedback Pedro.
I use LaTeX, instead of Word. Once you get the hang of it, it’s very worthwhile. I did the tips and tricks edition in apple pages, because it’s difficult to create designs like this in LaTeX. Having said that, it was quite difficult to do it pages as well. I think quark is the professional package for creating magazine-like documents but I don’t have access to that.
I do like the idea of open science - the more I think about it.
I hope that journals would be prepared to go out on a limb to discuss it. I’m sure open access ones would be more keen to than proprietary ones. But there are also open science leaders such as Jean-Claude Bradley and Rosie Redfield
Hosting in on the Nodalpoint wiki is a good idea too. I don’t want participants to get the impression that this would be something that “belongs” to me or bioinformatics zen, and hosting it on this website might do that.
June 29th, 2007 at 12:30 pm
Hi- jumping in a little late, but I saw you set up a wiki at nodalpoint that might find an appropriate home at http://openwetware.org/wiki/Main_Page ?
I’m not very versed in wikiquette but the open science idea starts not only by freely sharing the finished results (already a good start!) but also by sharing the tools developed to get there in an easily accessible format. The “web cookbook” that Neil mentioned in the first comment would definitely be welcome in the Protocols or Resources section - it should not just be about molecular biology, especially since molecular biologists need and use bioinformatics tools.
July 2nd, 2007 at 3:38 pm
Hi Athena,
I did set up a couple of pages at Nodalpoint. I’d be happy putting it on OpenWetWare, however it’s a bit scratchy so far, perhaps better off putting the final article there?
I think the idea of open science is very hazy at the moment, that’s why I believe discussion would benefit everyone. I completely agree with you when you said that everything should be made available not just the end product. I think the latter is open access, and the former is open science. But this is me being pedantic about words, the spirit is about sharing ideas and data for the sake of science, leaving behind the secrecy and paranoia that is the result of politics and competition.
November 13th, 2008 at 2:55 am
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