Methods

Methods

How to obtain sharper gel bands than your neighbour; how to efficiently design probes for microarrays; how to isolate as much RNA as possible;... Researchers describe proven experimental protocols that you won't find in standard manuals.

Plasmid repository Addgene (1.2012)
Centralised plasmid repositories may help researchers to better organise plasmid storage and sharing. Joanne Kamens, executive director of the non-profit plasmid repository Addgene, explains how it works and why Addgene is more than a simple repository... more
Guidelines to avoid peptide losses (7.2011)
Many researchers don’t give enough consideration to the material of their tubes and containers they use for handling and storage of peptides. This may have dire consequences. ... more
Digital Bookshelves (6.2011)
Some of our readers may remember what drafting a manuscript was like before the days of reference managers. Citations had to be put in by hand, double check made against the bibliography and this was done every time a piece of text was added or taken out. Boring, time-consuming and error-prone. “But we were happy in them days.” Really?... more
A practical guide to Next Generation Sequencing platforms (5.2011)
Chuck Berry, in an earlier generation, once wrote a song called the 13 Question Method that offers some guidance on finding the way to a girl’s heart. Today Karl Gruber asks nine questions that may directly lead you to decide, which Next Generation Sequencing platform to set your heart on... more
Bayesian statistics (4.2011)
In a recent bench philosophy feature we explored right and wrong ways to conduct the most common statistical tasks. In this issue, we will look at another statistical method that takes a completely different approach: Bayesian statistics... more
Phylogenetic analysis programme iPhy (3.2011)
We have had iPhones and iPads, now we have iPhy – a new web-based phylogeny server that takes the sweat out of bioinformatics. You keep hearing about it and you know it is there. That wealth of data hidden in the data pile. To get it, you need specialised computing skills — but you’re a biologist, not a computer programmer. If yesterday’s challenge was getting data, today’s challenge is being able to use it effectively. Take phylogeny, for instance... more
X-ray data collection in protein crystallography (2.2011)
Diffraction concepts are a headache for novice crystallographers and the underlying mathematics can be sometimes tricky but, after spending a reasonable amount of time studying the phenomena, it suddenly becomes clearer. ... more
Statistical Pitfalls (1.2011)
Politicians exploit it. Psychologists love it. Journals reject papers over it. But for many of us statistics is a bit like sleep – something we have to do but no-one really quite knows why. Here is a set of heuristics – some simple rules of thumb to avoid frequent stats failures ... more
Protein crystallization technique (6.2010)
There is a saying around structural biologists, that protein crystallization is half art and half science. Like science, however, every art is not only based on talent but also on hard work and practice. ... more
NMR spectroscopy vs. X-Ray crystallography (5.2010)
Nuclear magnetic resonance spectroscopy (NMR) and X-Ray crystallography are the main techniques to solve protein structures. Though some crystallographers still hold some reservations against NMR, it is well accepted among structural biologists that both methods may complement each other to get a better picture of a given protein structure ... more
Communicating science (4.2010)
Science today demands that researchers convey their findings to the society. Rhiannon Meredith and Johannes Hjorth, from the Centre for Neurogenomics and Cognitive Research within the VU University Amsterdam, explain how to share research with the scientific and general community. ... more
Yeast recombinational cloning (3.2010)
Yeasts have developed a highly efficient homologous recombination system. Researchers may take advantage of it, to easily clone their gene of interest. ... more
Scientific blogs (2.2010)
Life science blogs have sprung up like mushrooms in recent years and the list of researchers running their own blog is getting longer and longer. Steven Buckingham has checked, which blogs are worth reading. ... more
Next generation sequencing software (1.2010)
The Sanger method of sequencing caused a revolution in every corner of biology. With the recent emergence of Next Generation Sequencing, it is happening all over again. ... more
Patch clamp guidelines (6.2009)
Nearly 20 years ago Bert Sakmann and Erwin Neher were awarded the Nobel prize for Physiology and Medicine for their invention of the patch clamp technique. Since then, various forms of patch clamping have become routine, and even labs without an electrophysiology background are kitting themselves out with a patch rig. ... more
Free lab software (5.2009)
When you bought PCs for your lab, they almost certainly arrived already set up with an operating system. But an operating system isn’t enough to get everything done. You need to buy applications and then things can start getting expensive. What about using free software? ... more
The art of literature searches (4.2009)
Searching for scientific literature has never been easier. Journals are keener at placing their content online, and search engines are getting smarter and more powerful. Sophisticated indexing and even natural language processing, mean that finding what you are looking for is only a mouse click away. But are you keeping up with it all? ... more
On badly and well-kept laboratory notebooks (3.2009)
The lab book is the most important, and yet usually the most neglected, piece of scientific apparatus we use. A wellkept lab book is not only an obligation, but an irreplaceable resource. A badly kept lab book (so badly kept as, for instance, not to exist in the first place) can be, indeed sometimes has actually been, a researcher’s downfall. ... more
Information portal OpenWetWare (2.2009)
Technology is slowly allowing scientists to take information distribution back into their own hands as demonstrated by OpenWetWare.org. Not only does it allow researchers to publish bits of information that do not fit in with the conventional channels of journals but it also serves as a platform to interact with other researchers in an environment that is not owned by a profit-seeking company. ... more
Ten tips for better oocyte recordings (1.2009)
The South African frog Xenopus laevis is one of the most prominent organisms in today’s laboratories. Its lab career commenced as an animal for pregnancy testing in the 1940’s and Xenopus laevis is currently a crucial model organism for developmental biologists and electrophysiologists. ... more
Visualisation of experiments – Put your Paper onto Video (6.2008)
No scientist could have possibly missed the societal developments which are now slowly seeping into the scientific community. Open Access (OA) describes the movement to make publicly funded research ... more
The art of preparing effective scientific illustrations (5.2008)
We all know that effective communication is an essential skill in science. The ability to write in such a way that the reader is able, with the minimum possible effort, to grasp clearly what you are trying to say is a skill we rightly spend many hours perfecting. Sadly, much less attention is often paid to visual literacy – the art of preparing scientific figures. ... more
Open source for open minds. The EMBOSS Suite (4.2008)
Commercial bioinformatic programmes like the genome database and sequence analysis programme GCG, sold by the software company Accelrys, are both expensive and restricted in use or programme modification. There is no chance to independently change the source code of such proprietary programmes or even to fix the toughest bugs. In recent years, however, highly efficient open source programmes, such as the EMBOSS suite, have emerged that challenge commercial bioinformatic programmes like GCG. ... more
Time Managementand the State of Flow (3.2008)
Do you have too much to do and too little time to do it all in? Constantly running up against deadlines and unimpor-tant jobs seeming to take up too much of your precious time? If so, you may well be tempted to turn to TM ... more
Writing a short biography (2.2008)
A good print advertisement should be well written and tailored to the type of media and possible readers. The same applies to a short biography; it needs to be good to successfully promote a scientist and to communicate desired information to the intended audience. ... more
UK Biobank (1.2008)
UK Biobank processes thousands of blood and urine samples each day as part of a long-term initiative aimed at improving the prevention, diagnosis and treatment of a wide range of serious illnesses including cancer, heart disease, diabetes, arthritis and forms of dementia. ... more
Presenting Posters (5.2007)
Like actors and starlets walking along the red carpet at the Cannes Film Festival, researchers presenting their work at the poster session during a congress lecture break only have a single chance to attract the observer's attention. ... more
Design of efficient websites (4.2007)
On a lot of websites, including scientific ones, you can see warnings, that the page is not ready. Others are ready, however, they are harder to penetrate than a jungle. Geoffrey Richards and Guntram Bauer from the Human Frontier Science Program report on their experiences with academic websites and give some advice for website design. ... more
Discovering brain activity with
Near Infrared Spectroscopy (3.2007)
An old dream of mankind is to read the thoughts of another person. There have been many ideas in history on how to study the thoughts of a human being, which have led to the creation of mind machines or lie detectors. However, we are far away from reading a mind like a paperback but some techniques used today are well established and have quite an impact on understanding the brain. ... more
Picture presentation (2.2007)
Eye-catching illustrations symbolise the cherry on the cake of a scientific publication or presentation. If you flick through scientific papers, however, you often find hard-to-grasp figures and pictures. ... more
Polyacrylamide gel electrophoresis
without stacking gel (1.2007)
What motivates people who dedicate their time to developing methods? Is it the desire to help one's colleagues? Is it the urge to play? Sometimes the true driving forces appear a little different and odd. ... more