Catching up on the news after being away for two weeks - Lawrence Krauss had short comment in the New Scientist, Stop creationists undermining school science. The very quote-worthy punchline being:

Say that you are in charge of developing a state-wide high-school curriculum in French-language studies, and that you need the advice of a group of experts on how to put together the ideal programme. Is it better for officials to appoint these people, or for the public to vote on who they regard as the most attractive candidates for the job?
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Efficient time management is essential if you are to get the most out of your time in the lab. Breaking down projects into individual tasks and planning out when to do them is relatively easy. But the thing I find most difficult is accurately estimating the amount of time to allocate for each task.

I tend to be ridiculously optimistic with my estimates, so experiments and other tasks always take longer than I expect, resulting in a mad rush to get things finished at the end of the day.

But (as is often the case) Steve Pavlina has the solution. Read more »

Is it just me who thinks that biology researchers can be a bit sloppy when it comes to making and dispensing reagents accurately? Analytical chemists would laugh at our faith measuring cylinders for anything other than fairly rough work like making up media.

When it comes to more accurate work, like making up assay standards, measuring cylinders just just don’t cut it anymore. Here are a few ways to ensure that your stock solutions/standards are as accurate as possible, allowing you to get your experiments off to the best possible start.

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If you’ve been interested in the Folding at Home project, but wanted to play a much more active role then your wait is over. Join Fold It!

Protein structure prediction: As described above, knowing the structure of a protein is key to understanding how it works and to targeting it with drugs. A small proteins can consist of 100 amino acids, while some human proteins can be huge (1000 amino acids). The number of different ways even a small protein can fold is astronomical because there are so many degrees of freedom. Figuring out which of the many, many possible structures is the best one is regarded as one of the hardest problems in biology today and current methods take a lot of money and time, even for computers. Foldit attempts to predict the structure of a protein by taking advantage of humans’ puzzle-solving intuitions and having people play competitively to fold the best proteins.

I came across this interesting project from the HHMI Research News article.The game is a project developed by the Baker Lab.You can find more details about the game here. Have fun folding!

Your pipettes are probably most used tools in your lab and (I’ve said it before, but it’s worth repeating) without accurate pipetting you are asking for problems with your experiments.

Pipette manufacturers quote accuracy of pipettes but the truth is that pipetting accuracy is a very personal thing. It depends not only on the condition of your pipettes but also on your own pipetting technique.

It’s a very useful exercise to periodically measure your pipetting accuracy because this error is incorporated into every pipetting action you perform in the lab. Read more »

The Stanford Encyclopedia of Philosophy has a great article that I found recently on Reductionism in Biology. Synthesis, or holism, is nice and all, but you can’t really understand something without identifying and understanding its constituent parts. The intro below the fold…
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If you love spending time on Facebook, but want to keep on working while “Facebooking” (or whatever the correct verb is) don’t fear. Here are 4 (5) biology-related Facebook applications, most of which you can claim to be working while using.

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Here’s a video that might help prospective grad students out there. I came across it just doing a random search, but it’s a 7 and a half minute clip with grad students, faculty and staff of Duke University giving advice for you on your search Read more »

This week you get two “around the blogs” articles for the price of one!
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When you need to see the “big picture” in molecular biology then you need to take a look at the whole genome of the organism that are interested in.

From what I’ve seen, most people don’t do this; the general workplan that I’ve seen is that researchers only ever delve into the genome to look for a specific gene/protein sequence (unless of course their work involves genome analysis, phylogeny etc).

That’s a shame because not only does taking the whole genome view help you keep a perspective on the system you are working on, it can also be extremely useful for with strategies such as knock-ins and homologous recombination where having a rough idea of what surrounds your sequence of interest can be invaluable. So maintaining a good understanding of how to use them is a valuable tool.

A number of online and offline genome are viewers available, each with it’s own set of pros and cons. Here is an overview three that I have tried.

Artemis

Artemis is a genome viewer available from Sanger Institute. Its a java based tool with a 3-paned interface window that depicts the genome at various resolutions. Alternating between the different resolutions is a bit tricky but once you get a hold of it shouldn’t be difficult. There is a also search tool that allows your to track down the particular feature that you’re looking for.

A great feature of Artemis is that it allows you to edit the sequence annotations and features. Although the tool isn’t perfect and is a bit finicky at times, it gets the job done.

Artemis supports the most common filetypes -EMBL, GENBANK, FASTA or raw format. Extra sequence features can be added in in EMBL, GENBANK or GFF format.

The best thing I like about Artemis is that there is a web version as well as an offline version, which means once you get used to it you can run it on or offline on any computer anywhere that has java.

Apollo

Apollo genome viewer is another java based genome viewer and annotation tool. It is a part of the Gmod project which runs most of the online genome viewers. The tool came out of a collaboration between the Berkeley Drosophila Genome Project and The Sanger Institute.

Apollo has a similar set of features to Artemis provides, but I found the interface to be less user-friendly. But that’s just a personal opinion so you would be best to have a go at using both Artemis and Apollo and decide for yourself which is best. Again, the user guide will help you make best use of Apollo.

The NCBI Genome Workbench

The NCBI Genome Workbench is far more than just a genome viewer. As the name suggests, it is a complete and customizable workbench of tools that allow you to organize sequence data, which you can retrieve from NCBI databases or from your own files, for a project then view and manipulate them in a variety of ways. There is no online version available but downloading and installing NCBI genome workbench is quite simple.

The software allows you to view sequences as flat sequence files, phylogenetic trees, alignments and more.

The excellent zoomable graphics mode is the real strength of this package. It allows you to easily explore your sequence data at different levels of detail - individual genes can be viewed alone or in their genomic context and can be BLASTed straight from the graphical view. A nice set of alignment analysis tools is also available and BLAST and analysis results can be saved to your project making this a great way to keep track of your sequence data and analyses.

The tool supports quite a number of file formats, and I had no problems working with FASTA and most other file formats however when I tried to import the complete 1st chromosome of Dicyostelium which is in a GFF3 format the program kept crashing repeatedly, so clearly some bugs still need to be ironed out.

The NCBI genome workbench is a great idea, and provides a number of useful tools that make the program a must-have but the interface is a bit clunky and takes some getting used to. However, the site has a comprehensive set of instructions/tutorials to help you get up the learning curve quickly.

What’s your tool of choice?, drop us a line in the comments.

Photo: Semi-detached