[Taxacom] Software for curating taxonomic/biological/specimen information

Scott Thomson scott.thomson321 at gmail.com
Fri Dec 2 14:35:11 CST 2016


A small point on specify. First i like it and it is good software. I agreed
earlier with a previous recommendation of it.

All software has limits. First being effectively freeware means its long
term support is not garuntteed. This can become important as computer
systems advance. That is being a freeware no one is really being paid to
update it. So you have it while the will lasts.

Second it uses MySQL as a backbone database. This is a good database but is
basically the `lite` and free version of Oracle. It has limits,
particularly with the number of connections. This creates user, access and
data limits. I imagine this lead to the earlier querie of how many
instances of specify were being used for 40 million specimens. I would
imagine it is a few. What i generally see is each collection at an
institution (icthiology, herpetology etc) has its own instance. It is
necessay because of the limits.

Like all programs it has crashes, memory leaks etc, particularly after
shell or graphics updates. The speed at which patches and updated are done
to fix this is always slower in freeware than payware. Reality of any
software you get what you pay for.

Ok in an ideal world each museum will hire the staff and buy Oracle and
develop its own software designed for that institution. The cost of that is
ridiculous. So we are left with the alternative.

So above is the downside of Specify, i still recommend it. It does the job,
easy to use, intuitive, can datadump. The last is important if you ever
have to ditch it. Eventually the people maintaining it, which is probably
not their main job will stop. Once support stops it will become retro.
Which is the issue that started this thread.

Just so people get where i come from. Yes i am a biologist, its my job. But
i also have a software engineering degree. So i am saying the above from a
programmers perspective.

Cheers Scott

On Dec 2, 2016 4:36 PM, "John Bruner" <jbruner at ualberta.ca> wrote:

> In answer to Mike Sadka's question, here is an email I received from Robert
> H. Robins, the Collection Manager of Ichthyology of the Florida Museum of
> Natural History at Gainesville about 2 years ago.
> *******snip*********
>
> Hi John,
>
> Yes, we use Specify, the NSF supported software. We made the conversion
> from Microsoft Access in February of this year and I find it outstanding.
>
> If you can digitize it, you can have it in your database with Specify. I
> now link Collection Objects to images, reference works, and maps.
>
> View our Specify web portal here:
>
>
>
> http://specifyportal.flmnh.ufl.edu/fishes/
>
>
>
> Best thing to happen to my workflow/the collection since I began working
> here 18 years ago.
>
> All collections data at the Florida Museum (*40 million collection
> objects*)
> are being migrated to Specify. Complete so far are Fishes, Herps, Mammals,
> and Invertebrate Paleontology.
>
> Here’s more on Specify; I’ve also taken the liberty of copying the Director
> of the Specify initiative, Jim Beach:
>
>
>
> http://specifysoftware.org/
>
>
>
> And yes, it is free.
>
> (Oh and one last thing – there’s a weekly live on-line tutorial – in fact,
> it is going on as we speak!).
>
> Rob
>
> Robert H. Robins
>
> Senior Biologist/Collection Manager
>
> Division of Ichthyology
>
> Florida Museum of Natural History
>
> 1659 Museum Road
>
> PO Box 117800
>
> Gainesville, FL 32611-7800
>
> Office: (352) 273-1957
>
> Fax: (352) 846-0287
>
> rhrobins at flmnh.ufl.edu
>
> www.flmnh.ufl.edu
>
> *******snip*********
>
> --
>
> On Fri, Dec 2, 2016 at 10:27 AM, Nico Franz <nico.franz at asu.edu> wrote:
>
> > We can help set up arthropod collections here:
> > http://symbiota4.acis.ufl.edu/scan/portal/collections/index.php for a
> try
> > out. E-mail me. Cheers, Nico
> >
> > Beyond SCAN, this list of portals
> > http://symbiota.org/docs/symbiota-introduction/active-symbiota-projects/
> > is
> > no longer exhaustive but we have a pretty good idea of what's out there.
> > _______________________________________________
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> >
> > Injecting Intellectual Liquidity for 29 years.
> >
>
>
>
> --
>
>         John
> *******************************************************
> * Mr. John C. Bruner                                  *
> * Department of Biological Sciences                   *
> * University of Alberta                               *
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> * T6G 2E9  CANADA     /_ @  > />...w...w...w.....==== *
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> * VIRTUAL FAX: (780) 492-2216                         *
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> >
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