Bioperl: Re: Open Source and Bio questions

[Alessandro Guffanti]

Clay Shirky wrote:
 
> So they're more like venture capitalists with really tight relations
> with their partners, then?

Why not ? They may even end up buying you if your technology works well
(see recent acquisition from Pharmacia & Upjohn of a small Californian
biotech specialized in Cancer research).
 
> OK, so if they have sequenced, say, a bacterium I want the information
> on, I can either a) pay for access to the database or b), resequence
> it myself from scratch, no? I understand that with current technology,
> the database access is the cheaper choice, but for how long? With the
> $ per base pair figure dropping, whats to stop me from just
> resequencing the data I don't want to pay for?

Geee, you are a bit optimistic about the effort required for sequencing
even a small genome ! You need to have a genetic map, a physical map,
lot of skilled technicians and scientists, lots of good quality DNA,
complete coverage of all the genome .. don't think that sequencing an
organism is just pouring a mixture in a sequencher, there is a whole lot
to do before and after of that which is not easy, nor cheap, nor
straightforward for the moment.

If you are a company and are interested in a particular bacterial genome
because you want to make a new antibiotic against a resistant strain,
and this genome is protected by patents, no way, you have to subscribe
to. let's say, HGS database and pay a roialty. If you are  a scientist
and are interested in the same bacteria because you work at WHO or
wherever you should probably be able to access the information free (see
what TIGR does) but this is not often the case.
 
> Thats whats bugging me too - if I patent a sequence thats also in the
> public database, what do I own, or more realisitically, whjat
> behaviors can I sue people over?

I suppose if you make money of it you could end up to pay a roialty.
And if you are an University you will never be free to eventually file a
patent based on human genetic sequence anymore ( see UC vs. genetech
patent issue to get an idea:
 http://www.genentech.com/pressrelease/1999/11_19_0859AM.html
)
 
But a patent is meaningful only if you are patenting something *new*, so
that if the sequence was available *before* you actually sumbitted it to
the EPO or wherever .. it's too late ! The patent examiner runs a Blast
and FastA exactly as we all do, only vs. different databases which do
include information not publicly available.

The point is that primary information should be available to everybody,
in a good quality and in a good shape. If you own the Royal gardens
sooner or later
you may ask a ticket for entrance ..
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