Diatom group database


leszekwolnik <leszek@...>
 

Hi

I haven't been participating in the database / image reference discussion as I had been hoping to come to the group with a firm suggestion but want to speak up now as, so far, I'm slow in achieving my goal.

I think the thinking in the group is spot on and we need to examine the setting up of a repository of information and images. There will be good data and information generated by the group and I think Dick is the most shining example of what can be achieved - not bad for an 'auld wan', as we say here in Dublin!

We should be careful though as we need to build in sufficient parameters and flexibility to allow for the hosting of several (many!) thousand images, to allocate taxonomy, synonyms, physical, ecological and genetic characteristics, not to mention the damned literature.

How to search and access this easily, quickly and over the web?

I think that we might best be served by a Filemaker database and have been trying to program one myself but it is beyond my capabilities when it comes to automatically assigning correct synonymy and automatically pulling up all cross references and ecological preferences.

I'm trying to source an existing database for my own website and hope to publish it using Filemaker Server Advanced. If I can get the server installed then I would have no objection to hosting the groups database if the group wanted to take that route? There is a terrific database called Mantis, the scope and quality of which would be my aspiration for a diatom database.

You might think that this is too much of a stretch and that we should walk before we run but I would love to see us pull something of this quality and sophistication into being.

Another route would be to see if we could get a copy of Alexander Wolfe's database as it contains most if not all of what we'd require excepting for a bibliography module which I could add:-

http://www.chrono.qub.ac.uk/inqua/news19/n19-ehj.htm

He has offered to send on the template but is away on sabbatical leave at present. Does anyone else know of anyone who might have a copy of this? Even an empty clone with no records would be could as I could import the newest and updated version of Diatcode.


Hope this is of interest...?

Leszek

--- In diatom_forum@..., "Rob Kimmich" <kimmich46@...> wrote:

I think I hear a call for "diatom informatics". Of course, there are a lot of good sites out there, professional and otherwise, but maybe we are starting to think about a learning tool for this forum. To me this suggests a database, simple web page for displaying, and an image store that the database would call. All this would need a home, a way to ftp things, and folks to maintain everything. Starting to sound like AlgaeBase! For me there is always the tension between doing the biology and doing the data and image work. I find the latter quickly encroaches on the former.

Rob K

----- Original Message -----
From: Keith Shaw
To: diatom_forum@...
Sent: Sunday, April 03, 2011 8:04 AM
Subject: [diatom_forum] Species comparison scheme




As a novice "diatom indentifier" I have returned to trying out some simple visual comparison schemes.
One such scheme, with a scrolled HTML presentation of reference diatom images alongside a typical image, is now posted:
http://groups.yahoo.com/group/diatom_forum/photos/recent/1873938510/view

This particular image is from a Redondo Beach locality slide prepared by Raymond from a Chappell collection fossil sample. It's a 573x573 crop based upon a Tucsen 5 Mpixel image.

I'm thinking that based upon Rob's conversion of Dick's accurate list of Monterey formation marine diatoms, it may be worthwhile to generate a set of matching reference images to allow a scrolled comparison scheme?
We note that Reference Data and Additional Images can be easily added to the HTML template, should group members make such information available.

I would be interested in any comments.

-Keith


leszekwolnik <leszek@...>
 

Just reading my message and I made a error in that the paper states Dr Wolfe will send on the template on request - I haven't managed to contact him yet!

I also forgot the Mantis link!

http://insects.oeb.harvard.edu/mantis/

Regards


Leszek

--- In diatom_forum@..., "leszekwolnik" <leszek@...> wrote:


Hi

I haven't been participating in the database / image reference discussion as I had been hoping to come to the group with a firm suggestion but want to speak up now as, so far, I'm slow in achieving my goal.

I think the thinking in the group is spot on and we need to examine the setting up of a repository of information and images. There will be good data and information generated by the group and I think Dick is the most shining example of what can be achieved - not bad for an 'auld wan', as we say here in Dublin!

We should be careful though as we need to build in sufficient parameters and flexibility to allow for the hosting of several (many!) thousand images, to allocate taxonomy, synonyms, physical, ecological and genetic characteristics, not to mention the damned literature.

How to search and access this easily, quickly and over the web?

I think that we might best be served by a Filemaker database and have been trying to program one myself but it is beyond my capabilities when it comes to automatically assigning correct synonymy and automatically pulling up all cross references and ecological preferences.

I'm trying to source an existing database for my own website and hope to publish it using Filemaker Server Advanced. If I can get the server installed then I would have no objection to hosting the groups database if the group wanted to take that route? There is a terrific database called Mantis, the scope and quality of which would be my aspiration for a diatom database.

You might think that this is too much of a stretch and that we should walk before we run but I would love to see us pull something of this quality and sophistication into being.

Another route would be to see if we could get a copy of Alexander Wolfe's database as it contains most if not all of what we'd require excepting for a bibliography module which I could add:-

http://www.chrono.qub.ac.uk/inqua/news19/n19-ehj.htm

He has offered to send on the template but is away on sabbatical leave at present. Does anyone else know of anyone who might have a copy of this? Even an empty clone with no records would be could as I could import the newest and updated version of Diatcode.


Hope this is of interest...?

Leszek


--- In diatom_forum@..., "Rob Kimmich" <kimmich46@> wrote:

I think I hear a call for "diatom informatics". Of course, there are a lot of good sites out there, professional and otherwise, but maybe we are starting to think about a learning tool for this forum. To me this suggests a database, simple web page for displaying, and an image store that the database would call. All this would need a home, a way to ftp things, and folks to maintain everything. Starting to sound like AlgaeBase! For me there is always the tension between doing the biology and doing the data and image work. I find the latter quickly encroaches on the former.

Rob K

----- Original Message -----
From: Keith Shaw
To: diatom_forum@...
Sent: Sunday, April 03, 2011 8:04 AM
Subject: [diatom_forum] Species comparison scheme




As a novice "diatom indentifier" I have returned to trying out some simple visual comparison schemes.
One such scheme, with a scrolled HTML presentation of reference diatom images alongside a typical image, is now posted:
http://groups.yahoo.com/group/diatom_forum/photos/recent/1873938510/view

This particular image is from a Redondo Beach locality slide prepared by Raymond from a Chappell collection fossil sample. It's a 573x573 crop based upon a Tucsen 5 Mpixel image.

I'm thinking that based upon Rob's conversion of Dick's accurate list of Monterey formation marine diatoms, it may be worthwhile to generate a set of matching reference images to allow a scrolled comparison scheme?
We note that Reference Data and Additional Images can be easily added to the HTML template, should group members make such information available.

I would be interested in any comments.

-Keith


Rob Kimmich <kimmich46@...>
 

Leszek,
 
Thanks for the database comments and links. It's interesting how people set up their data behind the scenes.
 
You're right about taking our time in setting up something for the forum. Its purpose and who will maintain it seem central. Then there's always the discussion about what to use. Will it be Windows-based, Mac-based, or something else? I believe the most-used database software on the web now are MS-Access and mySQL. (During my database career, I watched a single Access table grow to one million rows with no performance degradation over a network.) My beginning site (micro.chemeketans.org) uses MS-Access. AlgaeBase uses mySQL. Sarah Spaulding at Diatoms of the United States (westerndiatoms.colorado.edu) has this to say.
 
"Although the original intent was to modify previous PHP code and a MySQL database schema that Lubinski [their programmer] created for our Antarctic Diatoms website (http:// huey.colorado.edu/diatoms), we deviated substantially from that plan. We realized that the long-term success of the western USA diatoms site meant that we had to make it simpler to update than the Antarctic site, which requires making changes to a fairly complicated relational database, FTP file uploads, and other somewhat technical procedures. Moreover we needed to add blog-like functionality to help promote communication with peers to help “fix” diatom identification problems. The easiest solution to all of those issues was to use a Content Management System (CMS). We re-aligned our back-end development plan to center on a CMS. Lubinski chose a commercial CMS, which runs on PHP and MySQL."

I don't know that we want to make the commitment to a CMS or to mySQL, but it's good to see what is being done out there. (Their Antarctica site is interesting in itself!)
 
Maybe we can ride along on your Filemaker efforts. We would want at least one person to back you up!
 
Rob K
 

----- Original Message -----
Sent: Monday, April 04, 2011 6:44 AM
Subject: [diatom_forum] Re: Diatom group database

 

Just reading my message and I made a error in that the paper states Dr Wolfe will send on the template on request - I haven't managed to contact him yet!

I also forgot the Mantis link!

http://insects.oeb.harvard.edu/mantis/

Regards

Leszek

--- In diatom_forum@..., "leszekwolnik" wrote:
>
>
> Hi
>
> I haven't been participating in the database / image reference discussion as I had been hoping to come to the group with a firm suggestion but want to speak up now as, so far, I'm slow in achieving my goal.
>
> I think the thinking in the group is spot on and we need to examine the setting up of a repository of information and images. There will be good data and information generated by the group and I think Dick is the most shining example of what can be achieved - not bad for an 'auld wan', as we say here in Dublin!
>
> We should be careful though as we need to build in sufficient parameters and flexibility to allow for the hosting of several (many!) thousand images, to allocate taxonomy, synonyms, physical, ecological and genetic characteristics, not to mention the damned literature.
>
> How to search and access this easily, quickly and over the web?
>
> I think that we might best be served by a Filemaker database and have been trying to program one myself but it is beyond my capabilities when it comes to automatically assigning correct synonymy and automatically pulling up all cross references and ecological preferences.
>
> I'm trying to source an existing database for my own website and hope to publish it using Filemaker Server Advanced. If I can get the server installed then I would have no objection to hosting the groups database if the group wanted to take that route? There is a terrific database called Mantis, the scope and quality of which would be my aspiration for a diatom database.
>
> You might think that this is too much of a stretch and that we should walk before we run but I would love to see us pull something of this quality and sophistication into being.
>
> Another route would be to see if we could get a copy of Alexander Wolfe's database as it contains most if not all of what we'd require excepting for a bibliography module which I could add:-
>
> http://www.chrono.qub.ac.uk/inqua/news19/n19-ehj.htm
>
> He has offered to send on the template but is away on sabbatical leave at present. Does anyone else know of anyone who might have a copy of this? Even an empty clone with no records would be could as I could import the newest and updated version of Diatcode.
>
>
> Hope this is of interest...?
>
> Leszek
>
>
> --- In diatom_forum@..., "Rob Kimmich" > >
> > I think I hear a call for "diatom informatics". Of course, there are a lot of good sites out there, professional and otherwise, but maybe we are starting to think about a learning tool for this forum. To me this suggests a database, simple web page for displaying, and an image store that the database would call. All this would need a home, a way to ftp things, and folks to maintain everything. Starting to sound like AlgaeBase! For me there is always the tension between doing the biology and doing the data and image work. I find the latter quickly encroaches on the former.
> >
> > Rob K
> >
> > ----- Original Message -----
> > From: Keith Shaw
> > To: diatom_forum@...
> > Sent: Sunday, April 03, 2011 8:04 AM
> > Subject: [diatom_forum] Species comparison scheme
> >
> >
> >
> >
> > As a novice "diatom indentifier" I have returned to trying out some simple visual comparison schemes.
> > One such scheme, with a scrolled HTML presentation of reference diatom images alongside a typical image, is now posted:
> > http://groups.yahoo.com/group/diatom_forum/photos/recent/1873938510/view
> >
> > This particular image is from a Redondo Beach locality slide prepared by Raymond from a Chappell collection fossil sample. It's a 573x573 crop based upon a Tucsen 5 Mpixel image.
> >
> > I'm thinking that based upon Rob's conversion of Dick's accurate list of Monterey formation marine diatoms, it may be worthwhile to generate a set of matching reference images to allow a scrolled comparison scheme?
> > We note that Reference Data and Additional Images can be easily added to the HTML template, should group members make such information available.
> >
> > I would be interested in any comments.
> >
> > -Keith
> >
>