Handling genetic and biological data requires bioinformatics

In the last decades, much biological work has moved from the field or wetlab to the computer. Genetic data have changed from a few allele sizes and short DNA sequences to genomic datasets that may be sized many gigabytes. Fieldwork is nowadays often supported by automatical GPS geolocating, laser or radar scanning, and other techniques also creating large datasets. Such data require specialized software and experienced operators for suitable handling.

Bioinformatics are computationally demanding

Most business or home computers will not have sufficient processor power and memory to work with biological datasets. Furthermore, most of these computers will run operating systems that are not very good in these tasks. If some software can be executed on them, it will result in day- or even weeklong processing times. Thus, large machines with many processing cores, the ability to run processes in parallel, big memory, and fast SSD storages are required.

These tasks are best done in unixoid operating systems

From its beginning, Unix was designed as a multitask, multiprocessor operating system that can address almost infinite amounts of memory. Today, many derviates of the original Unix exist, with Linux being the most prominent one, used on most high performance computers. We use Linux Mint and CentOS operating systems.

The Linux command line is the natural habitat of the bioinformatician

Most bioinformatic applications lack a graphical user interface. This has one simple reason: it is not needed. Even more, graphical interfaces inhibit automated processing and efficient pipelining between applications. With a deep understanding of the command line and its powerful tools like grep, awk, and sed, data handling is usually done much faster than it could ever have been done with a GUI and a mouse.

The effort for understanding bioinformatic applications can be big, and experienced informaticians are hard to get

Many bioinformatic software lacks almost any documentation. The other extreme, thousands of pages of documentation, that make it almost impossible to filter the few really relevant passages, is also frequent. The usual workaround is to search for online forums where these topics are discussed. It may cost a student weeks or months to finally use an application really productive. Experienced operators are rare and usually only availabe for long-term postdoc contracts. They will rather not engage in smaller projects.

We prefer open software and are open to our customers

At bioformconsult, we are big fans of free software ("free" as in "free speech", not as in "free beer") and open source code. When a task can be done either in an open or propietary environment, we will always chose the open one. Our customers will, together with their results, receive all scripts we built to achieve them and full computational protocols.

To fulfil your bioinformatic needs is our mission

So it is.