IUBio

Sequencing Facility trends

Tania Tania
Fri May 16 07:58:52 EST 1997


Hello!

My name is Tania Broveak and I am an independent consultant in the area 
of bioinformatics and medical informatics.  You may see my name on 
software reviews or on articles summarizing trends in the 
bioinformatics industry.

Currently, I am trying to understand some of the fundamental changes 
taking place in the auto-sequencing lab.  It appears that the nature of 
sequencing facilities is changing and I hope that this survey will 
help me better understand those changes.

The enclosed survey attempts to capture 
	* trends in sequencing and the services your lab 
	  offers, as well as 
	* trends in the use of computer software in the automated
	  sequencing lab.

I apologize for the length of the survey, but felt all aspects of the 
auto-sequencing lab should be considered for a complete 'picture'.  All 
responses are greatly appreciated.

Deadline for responses:  Thursday, May 22
Please send responses by email (taniab at iafrica.com) 
		   OR by fax  (402) 987-9922

The survey results will be posted back to the newsgroup shortly after the 
conclusion of the survey.  I expect to have them tabulated and posted by 
Tuesday May 27.

Thank you very much!

Tania Broveak
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---------------------------------------------------------------------
         SURVEY: TRENDS IN THE AUTOMATED SEQUENCING LAB
---------------------------------------------------------------------

Name: ____________________ (optional)
Title:____________________
Organization:_____________
Phone:____________________ (optional)
Email:____________________ (optional)

-------------
All about you
-------------

* Describe your role:


* How many years have you held this role? ______ yrs.

------------------
Laboratory Profile
------------------

* Would you consider your facility to be a:
  ____ High throughput lab
  ____ Core sequencing facility
  ____ Other (describe): _______________

* What type of projects are you typically running?
  (mark all that apply)
  ____ ESTs		 	____ genomic sequences	
  ____ high coverage	 	____ low pass		
  ____ shotgun		 	____ walking
  ____ whole genome scan 	____ positional cloning
  ____ expression studies       ____ other _______________

* What is the current throughput of your lab?  
  ____ lanes/day

* How many sequencers do you have at your facility? ______

  What type/model?  
     #      Maker	        Model 
  ------    ------------        ---------------------------
   ____     ABI		        __373  __377  __Other______
   ____     Pharmacia	        ___________________________
   ____	    Licor	        ___________________________
   ____     Molecular Dynamics  ___________________________
   ____     Other:		___________________________

* Are you scheduled to purchase additional sequencers in 1997?
  	____  Yes	____ No

    How many?  ______

    Have you already identified which make/model?
  	____  Yes	____ No

* How many technicians are in your facility? ___________
  What is their education/skill level?


* How many collaborators/projects does your facility serve?
    #________

* How many locations are these collaborators located at?
    #________

* What % are at a different site from your facility? _______%

* Do you perform any post-processing, assembly or analysis 
  on the resulting sequences?   ____ Yes    ____ No

* IF SO, which software packages do you use?

  Assembly:
  ____ Autoassembler	____ Sequencher	  ____ Phrap
  ____ Seqman (DNA*)    ____ GCG	  ____ GeneWorks
  ____ Other ___________________________

  Searching:
  ____ Blast 		____ Smith-waterman 
  ____ Fasta		____ Inherit
  ____ Other: __________________________

  Other: (describe)

* What is the #1 bottleneck for your facility?
  (try to check only one, but if more than one 
   applies strongly, feel free to mark those too)

  ____ number of machines    ____ personnel
  ____ workflow		     ____ post-sequencing analysis
  ____ sample tracking 	     ____ inventory mgmt.	
  ____ request tracking      ____ other (describe)


* What is your typical sample tracking error rate?______

* What other equipment or services is your facility responible for?
  ____ genotyping	____ expression analysis
  ____ synthesis	____ mapping
  ____ Other____________________________

* What % of your work is sequencing and what % is another type of
  work?
	_____% sequencing	____% other

* How does the profile of your lab's work differ from one year ago?


* How do you expect this profile to look one year from now?


* What other major equipment do you have in the lab?


----------
Automation
----------

* How do your collaborators interact with your facility?

  ____ paper forms   	
  ____ Web-based form
  ____ computerized form (___ Mac, ___ PC, ___ Mainframe)
  ____ other ____________________________________

  Details:


* How do you track the following inside your facility:

  - samples and projects
    ____ paper forms/files    
    ____ spreadsheet software
    ____ word processing software
    ____ specially-developed system
         ( ___ Mac, ____ PC, ____ Mainframe, ____ Web-based)
    ____ purchased software:____________________________
    ____ other

  - inventory
     ____ paper forms/files    
    ____ spreadsheet software
    ____ word processing software
    ____ specially-developed system
         ( ___ Mac, ____ PC, ____ Mainframe, ____ Web-based)
    ____ purchased software:____________________________
    ____ other

  - reports
    ____ paper forms/files    
    ____ spreadsheet software
    ____ word processing software
    ____ specially-developed system
         ( ___ Mac, ____ PC, ____ Mainframe, ____ Web-based)
    ____ purchased software:____________________________
    ____ other

* If any of the software you use includes a database, please
  note which one:
    ____ Sybase		____ Oracle	____ Informix
    ____ Filemaker Pro  ____ FoxPro     ____ MS Access
    ____ other

* What are your greatest pressures from collaborators and from 
  upper management?
    ____ increased throughput/efficiency
    ____ reduction in sample-tracking errors
    ____ providing value-added services, 
	  (describe)________________________________
    ____ other

* How does computer hardware and software fit into your facility?


* Does your company prefer to:
    ____ purchase ready-made software from commercial vendors
    ____ develop your own software in-house
    ____ commission customized software

* What is your facility's annual budget for hardware and software?
   ____ <$50,000	____ $50K-$100K
   ____ $100K - $500K	____ >$500K

* What in-house informatics resources do you have access to?
   #_____ people
   #_____ computers

* If I use the term "LIMS", what does that mean to you?


* Can you name 3 commercial "LIMS" software packages?
   1.  _____________________
   2.  _____________________
   3.  _____________________


------------
Perceptions:
------------

The following are simple statements describing trends in sequencing and 
related functions.  Please mark the answer you feel is most correct.

1.  Sequencing will become ____ more / ____ less important over
    the next year.
2.  Genotyping will become ____ more / ____ less important over
    the next year.
3.  Expression studies will become ____ more / ____ less important 
    over the next year.
4.  Improved workflow ____ will / ____ will not reduce time and cost
    in my facility.
5.  Computers ____ are / ____ are not useful in improving laboratory
    workflow.
6.  If there were a software solution that improved the functioning
    of my facility, my company ____ would / ____ would not be 
    interested in evaluating it.


THANK YOU very much for your time and for your diligence in completing 
this survey.  I hope that you are looking forward to a report of the 
findings of this survey and that the resulting information can be useful 
to you and your company.

Please remember to email the survey to me directly (taniab at iafrica.com) 
rather than respond to the newsgroup to ensure your input is included.

Best regards,

Tania Broveak
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