[Obi-instrument-branch] instrument call tomorrow?

[Melanie Courtot]

Hi all,

Are we having an instrument call tomorrow?

If people are around it would be nice to discuss our list of core RU,
and potentially have plans to review/clean up the MSI terms Daniel
added before he leaves?

Thanks,
Melanie

---
Mélanie Courtot
TFL- BCCRC
675 West 10th Avenue
Vancouver, BC
V5Z 1L3, Canada

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[Melanie Courtot]

Hi,

I can do next week but then will be unavailable until after the meeting.

Shall we try and discuss our core terms list over email?

Cheers,
Melanie

On 13-Jan-09, at 4:35 AM, sch...@ebi.ac.uk wrote:

> Hello all,
> Sorry, can't attend todays call. I am in the midthst of removal
> stress. I
> will attend the calls again 2 weeks from now onwards.
> Cheers, Daniel Schober.

[Daniel Schober]

That's fine with me.
Cheers, Daniel.

Melanie Courtot wrote:

--
__________________________________________________________________________________________

Dr. Daniel Schober

NET Project - Ontologist

The European Bioinformatics Institute email: sch...@ebi.ac.uk
EMBL Outstation - Hinxton direct: +44 (0)1223 494410
Wellcome Trust Genome Campus fax: +44 (0)1223 494 468
Cambridge CB10 1SD, UK Room: A3-141 (extension building)

Project page: www.ebi.ac.uk/net-project

Personal page: http://www.ebi.ac.uk/Information/Staff/person_maint.php?s_person_id=734
Former home page: http://www.bioinf.mdc-berlin.de/%7Eschober/

[Melanie Courtot]

OK :)

In oder to get us started, here is an excerpt from the doc Daniel
added under SVN:
Instrument/Device

It’s hard to find a formal differentiae to distinguish ‘instrument’
from ‘device’. Humans tend to classify more in a probabilistic and
fuzzy way. It is hard to discretely model phase transitions that are
continuous.
In general an instrument is regarded to be more complex as a device.
Complexity is hard to define. Can a certain amount of ‘has part’
statements (min cardinality) lead to an acceptable solution ? Are
there approaches to model Entrophy? This also lead to the question if
a distinction between a device function and a instrument function is
justified. Do we need the device / instrument distinction at all? What
do we gain having this distinction? A simple device should not get all
the properties of an instrument. E.g. a 'tube' does not need to have
parameters, data outputs, software, .. that a 'flow cytometer'
instrument might have.

One question on which I am still a bit unsure is "do we need
distinction between device and instrument".

We seem to say that instruments should have restrictions that device
won't have - if this is the case it should be pretty easy to use those
to define the difference, i.e. if we say instruments have settings but
not device.

However and based on our past discussions there seemed to be some
ambiguity there, for example with the ultrasonic homogenizer (is it a
device or an instrument?)

Maybe an idea would be to use that example, see if we can reach
consensus, and maybe it will help us to define properly the 2 terms?

Melanie

[sch...@ebi.ac.uk]

Hello all,
Sorry, can't attend todays call. I am in the midthst of removal stress. I
will attend the calls again 2 weeks from now onwards.
Cheers, Daniel Schober.

[Frank Gibson]

On Tue, Jan 13, 2009 at 9:00 PM, Melanie Courtot <mcou...@gmail.com> wrote:
> OK :)
>
> In oder to get us started, here is an excerpt from the doc Daniel
> added under SVN:
> Instrument/Device
>
> It's hard to find a formal differentiae to distinguish 'instrument'
> from 'device'. Humans tend to classify more in a probabilistic and
> fuzzy way. It is hard to discretely model phase transitions that are
> continuous.
> In general an instrument is regarded to be more complex as a device.
> Complexity is hard to define. Can a certain amount of 'has part'
> statements (min cardinality) lead to an acceptable solution ? Are
> there approaches to model Entrophy? This also lead to the question if
> a distinction between a device function and a instrument function is
> justified. Do we need the device / instrument distinction at all? What
> do we gain having this distinction? A simple device should not get all
> the properties of an instrument. E.g. a 'tube' does not need to have
> parameters, data outputs, software, .. that a 'flow cytometer'
> instrument might have.

The differentia that stands out for me between a device and an
instrument would be that an instrument are those devices that produce
data

> One question on which I am still a bit unsure is "do we need
> distinction between device and instrument".

I would suggest it would be helpful using the distinction above. I
don't think you would call a test-tube or a petri-dish an instrument.

> We seem to say that instruments should have restrictions that device
> won't have - if this is the case it should be pretty easy to use those
> to define the difference, i.e. if we say instruments have settings but
> not device.

Settings are not enough and too vague. A lamp can have settings
(variable dimmer switch) does this make it an instrument? I would
suggest not.

> However and based on our past discussions there seemed to be some
> ambiguity there, for example with the ultrasonic homogenizer (is it a
> device or an instrument?)
> Maybe an idea would be to use that example, see if we can reach
> consensus, and maybe it will help us to define properly the 2 terms?

There can be the cases where people call certain devices, instruments,
where others will not and vice versa. I don't really feel devoting
alot of time to working out a complex definition of an instrument will
be of much benefit - especially not in Vancouver. My suggestion of a
way forward would be to define instrument as any device that produces
data and place an editor note on it saying something like this
definition may not cover all devices that people want to call
instruments and will be readdresses when strong case-studies to the
contrary are presented

Cheers

Frank

--
Frank Gibson, PhD
http://peanutbutter.wordpress.com/

[Ryan Brinkman]

>The differentia that stands out for me between a device and an
>instrument would be that an instrument are those devices that produce
>data

Best distinguishing explanation I can recall. YAY!

>> One question on which I am still a bit unsure is "do we need
>> distinction between device and instrument".

>I would suggest it would be helpful using the distinction above. I
>don't think you would call a test-tube or a petri-dish an instrument.

Agreed

Ryan