setting up a sequence analysis facility

Reinhard Doelz doelz at comp.bioz.unibas.ch
Wed Jun 10 05:00:57 EST 1992


It is interesting to see that more and more small labs want to own an 
independent sequence analysis facility. Despite the space (office) needed, 
staffing and investment are considerable. If you follow the growth curve
observed in the past two years, the resources will be under a considerable 
pressure with respect to changing technology. In particular, the renewal 
of hardware in the field has experienced much shorter intervals than earlier. 
I remember the time where a lonesome VAX730 was installed for five years before
the last job was submitted. Today, two years without new hardware endanger 
your competitiveness.  

In addition to hardware, the software used today is quite often underestimated
with respect to financial efforts. If you purchase GCG or IG or any other 
mainframe software on a workstation, you pay for a license once. Suddenly,
your customers want graphical user interfaces and you need ethernet cabling
with (at least) X Windows terminals or -emulators everywhere. At least in 
most institutes in europe, this is beyond reach for the VT100 type terminal
owners with respect to budgets and resources. Alternatively, some (Mac users 
in particular), swear on 'their' PC software. It can do most things (searches
are usually done elsewhere), and comes either as a what-you-get-is-what-
you-paid-for PD software, or and commercial. Both alternatives are 
attractive for small sites but also financially not easy to manage 
for 300 users. In addition, you will need to update, backup, and maintain 
300 PC's individually which are surely not configured identically. Again, 
a lot of manpower needed here. 

Last, staffing is needed to maintain data (and UPDATES). It is quite 
frequently just 'forgotten' that a molbio site isn't installed once, and 
runs forever afterwards. At least weekly maintenance (data updates), as 
well as user aid, is needed. I currently serve 300 users directly and 
much more via delivery of data. The illusion offered in many job ads that 
a researcher is looked foe who does maintenance of a molbio side in 
a few hours beside its normal work is still there but not realistic. 

Resumee: 
Think twice before you go for an own site. Either try to find a center close 
to you where you can buy into, or try to form a small community which 
shares costs and efforts. Moderate centralisation is a must these 
days if you want to survive. 

Maybe this helps. 

Regards 
Reinhard 

In article <BRIANF.92Jun9191220 at dna.uvm.edu>, brianf at dna.uvm.edu (Brain Foley) writes:
|> 
|> 1) Where did you obtain funding, and where did you try but fail to 
|>    obtain funding?
|> 
	local funding mostly, federal funding for 1 staff position (3 yrs). 
|> 
|> 2) How long did it take to get the facility up and running?
|> 
	starting 1986, about 1 year to get VMS reasonably well. Another 
	year for setting up the UNIX site in 1991. 
|> 
|> 3) What percentage of your budget goes toward software, hardware and 
|>    personnel?  
|> 
	running cost 80%  to maintenance of hw/sw. 
	Investment dto, staffing as well. 
	Total ratio approx. 1:1:5 running/investment/staffing. 
|> 
|> 4) What hardware do you currently have?
|> 
	Share of VAX8840/VAX6510 cluster, SGI 320 GTX, Crimson, 2 Indigos.
|> 
|> 5) What software do you currently have?
|> 
|> 
	GCG on VAX/VMS and UNIX proved to be the pest price/performance. 
	Also we use W.Pearson's FASTA package in some instances. 
	On VAX/VMS, also PIR software, and on UNIX, ACEDB. 
	BIOSYM for molecular modelling. 

|> 6) What hardware do you wish you could purchase next?
|> 
	More disks (currently in use: 2 GB on VMS, 4 GB on UNIX), 
	more backup media (currently, an exabyte on VMS and DAT on UNIX). 
|> 
|> 7) What software do you wish to purchase next? 
|> 
	I am quite satisfied with  what we currently have. 
|> 
|> 8) Do you sell usage time on your facility?
|> 
	I charge a 'contribution' for sites receiving data without 
	federal funding. This is the usual 'academic' fee . No 
	commercial users are permitted to use the facility, neither
	do I use commercial packages for preparing the data. 
	Otherwise, non-profit licenses are no longer valid. 
	We cannot afford for-profit licenses. 
|> 
|> 9) Do you buy usage accounts from other facilities such as the Pittsburgh
|>    Supercomputer Facility or Intelligenetics Suite?
|> 
	No - we ARE the center :-) 
|> 
|> 10) How much of your time is spent setting up user interfaces?
|> 
	1 staff position half-time
|> 
|> 11) Have you set up a gopher interface to Internet resources?
|> 
	yes.
|> 
|> 12) What is the most important advice you can give us?
|> 
|> 
	see the blurb at the top. 
|> 
|> --
|> ********************************************************************
|> *  Brian Foley               *     If we knew what we were doing   *
|> *  Molecular Genetics Dept.  *     it wouldn't be called research  *
|> *  University of Vermont     *                                     *
|> ********************************************************************

-- 
+----------------------------------+-------------------------------------+
|    Dr. Reinhard Doelz            | RFC     doelz at urz.unibas.ch         |
|      Biocomputing                | DECNET  20579::48130::doelz         |
|Biozentrum der Universitaet       | X25     022846211142036::doelz      |
|   Klingelbergstrasse 70          | FAX     x41 61 261- 6760 or 267- 2078     
|     CH 4056 Basel                | TEL     x41 61 267- 2076 or 2247    |   
+------------- bioftp.unibas.ch is the SWISS EMBnet node ----------------+
               -----------------------------------------




More information about the Bio-soft mailing list