Thank you xy for the kind introduction.
Hi! Welcome to the biology section of LinuxConf.AU. If you want to learn about
how new antibiotics are discovered, you've come to the right auditorium.

I'm going to present antiSMASH, the software I'm developing as a Ph.D. project.
It's open source software under the GNU GPLv3 (or later) and we're also running
a public instance for the scientific community to use.

But before I start talking about the software I'm working on, let me give you a
short primer on the biology side of things. Without that background, the rest
of the talk will be much harder to follow. Feel free to interrupt with
questions at any time.

As you might have seen on the first slide, I work in the Division for
Microbiology/Biotechnology at the Microbiology Institute of the University of
Tübingen, Germany. So, biotechnology, what is this all about?

The United Nations "Convention on Biological Diversity" defines biotechnology
as "Any technological application that uses biological systems, living
organisms, or derivatives thereof, to make or modify products or processes for
specific use". Quite a mouthful. But let me use a metaphor to build my
explanations on.

In biotechnology, we use biological systems such as bacteria or yeast, and then
turn them into little factories to produce things we want. A popular example
would be... beer. It's one of the oldest biotech applications on the planet. We
use a certain kind of yeast (Saccharomyces cerevisiae) to turn sugar into
alcohol and carbon dioxide. Another widespread example is the use of a
bacterium (Escherichia coli) to produce human insulin to treat people suffering
from diabetes.

Now, what's so nice about using those tiny organisms to produce these
substances instead of going for an all-chemical full synthesis? Well, the first
is that in some cases, like yeast producing ethanol, nature has already built
that functionality into the organism. It's much easier to just let the yeast do
it's thing that it would be to do the synthesis from scratch.

Using bacteria to produce human insulin is a different story. The bacteria
involved don't naturally produce insulin, they were engineered to do so.
However, there's another reason we're using biological systems to produce
stuff. Unlike a real factory, bacteria are self-reproducing. So if you provide
enough food, a tiny amount of starter bacteria will multiply, and then you have
a lot of little factories running your production line..