Sometimes there is a need to remove all the probesets, which have expression values below the minimal spike-in intensity on the Affymetrix microarray. The reasoning behind this procedure is simple: minimal-expression spike-ins represent the bottom margin of microarray sensitivity, and anything below that margin cannot be reliably quantified – which also means that both fold-change and p-value of expression variance will be unreliable for these probesets.

Here’s a simple R script to do just that. It is abundantly commented, and also contains an optional (commented out) fragment which allows the removal of more low-variance, low-intensity probesets.

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DIYbio is

an organization that aims to help make biology a worthwhile pursuit for citizen scientists, amateur biologists, and DIY biological engineers who value openness and safety.

DIYbio also has a google group, where a wide range of questions – from bio-patents to DIY gel electrophoresis shopping list and model organisms is dicussed. There is also a DIYbio/biohacking FAQ.

Today for me is the day of discoveries. I learned about the International Open Space Initiative (to give robotics enthusiasts a way to send their tele-controlled and/or intelligent robots to the Moon and Mars), about the DIYbio and biohackers, about OpenManufacturing (which doesn’t seem to have produced enough content to link to), Open Source Medicine (ouch!), BioBrick Assembly Kit (with an assembly manual), OpenWetWare, and a whole bunch of other awesome and inspiring community efforts, which do not belong here.

Do you feel the wind of change?

Stumbled upon SciVee.TV – an open video upload service for research-related videos.

I believe it is highly useful. Compare: watching an 8-10 minute video of someone’s research to reading their article on that same subject. For me, those 8-10 minutes make video option a clear winner.

One of the envisioned uses of SciVee is to upload videos describing peer-reviewed published articles. This has two benefits for the reader: quickly getting acquainted with the essence of the article, and having that article as a complete reference for any questions not discussed in the video. For the author, this gives an additional bonus of higher visibility of his research.

Personally, I’ve immediately found 3 videos pertinent to my topic. Of those, one was accompayning an article in PloS Biology, one was an hour-long lecture, and one was a poor quality audio recording of someone’s intended research.

SciVee is young, and that is currently the largest drawback: not much could be found in a narrow research field. But I’m sure it will grow.

Recently, I have come across an excellent piece of advice called Ten simple rules for getting published. The only thing I have to add is that final rule #10 should be kept in mind while checking through all the previous rules – e.g. when editing someone’s submission, make sure that you are in position to be the editor for that article, and make sure your decision will influence chief editor’s decision – otherwise there’s no use reviewing.

PLoS Computational Biology, where the “simple rules” were published, has a Ten simple rules collection, which includes a handful of other useful advice articles, like 10 simple rules for selecting a postdoctoral position.

Giovanni Dall’olio has recently posted a presentation on using make.

Although it has “bioinformatics” on the title page, this is a good and very easy to understand make intro.

Original post is here.

The following sites are available:

http://bacteria.ensembl.org
http://protists.ensembl.org
http://metazoa.ensembl.org

During summer, two more sites – for Fungi and Plants – should be made available.

Learn more about Ensembl Genomes project.

First, learn about custom CDFs and why they are needed.

The aroma.affymetrix R package google group has a how-to: create a CDF annotation file from scratch.

Also useful: how to convert CDF into an R package, which has all CDF data available (as a PDF with more details).

If you were a frequent user of GNF SymAtlas, then you’d better bookmark BioGPS – Your Gene Portal System. BioGPS is basically the same gene expression atlas, but with a completely different interface, and more flexible ideology (e.g. expression atlas is now just a “plugin”, and more of those can be plugged in).

There are also some easter-egg-like features: try hovering the BioGPS logo in the top left corner several times…

This in itself wouldn’t be so exciting, if it were not for the new webcode! If you do visit Ensembl now, you will be definitely surprised with the page loading speed – it is amazingly faster than it used to be! Also, as you dig deeper and deeper, you’ll see that there are a lot more other differences – starting with the new design, and not forgetting the changed page organization logic.

To cut the long story short, here’s the list of changes in the new Ensembl 51 webcode release. Other changes to Ensembl in release 51 are also available.

One of the new features which caught my attention is the ability to add custom tracks in Ensembl (which is a long-available feature in UCSC Genome Browser). Interestingly, you do not even have to be logged in to use this feature. We shall be considering providing the TFBS custom track for several species, as predicted de-novo by our evolutionary conserved tfbs search tool (binding site finder), but this is a long shot, given the already published COTRASIF development roadmap.

There is one more great news which is kinda insufficiently highlighted: the brand-new Ensembl Genome Browser website, which (as planned, it hasn’t yet started operations) will provide access not only to vertebrates, but also to other taxonomy groups. The full list is:

• Metazoa
• Protists
• Bacteria
• Plants
• Fungi

For some period of time, I had to switch to my Windows installation when writing articles with references, because I keep my references database there and there is an extremely convenient add-on for MS Office to insert citations and format bibliography on the fly.

However, it is quite inconvenient to make/run programs/scripts under Linux, and then switch to Windows to describe the obtained results in the article-like form. Thus, I briefly investigated available citation managers for Linux.
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