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  <title>All posts by Dave Lane: Dataversity</title>
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    <entry>
      <title>Integrated Biodiversity Management System</title>
      <link rel="alternate" type="text/html"
            title="Integrated Biodiversity Management System"
            href="http://dataversity.org.nz/r/post/6Q1i3twQ1Sd26MsBl018tR" />
      <id>http://dataversity.org.nz/r/post/6Q1i3twQ1Sd26MsBl018tR</id>
      <author>
        <name>Dave Lane</name>
        <uri>/p/lightweight</uri>
      </author>
      <updated>2012-07-26T22:23:52Z</updated>
      <summary type="xhtml">
        <div xmlns="http://www.w3.org/1999/xhtml">
          I thought Colin Meurk might respond to this one, but as I think he's in the field and out of email contact, I can tell you that Egressive's role in enhancing the iNaturalist platform is to substantially augment its observation (and other)&#8230;
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          <pre>I thought Colin Meurk might respond to this one, but as I think he's in 
the field and out of email contact, I can tell you that Egressive's role 
in enhancing the iNaturalist platform is to substantially augment its 
observation (and other) capabilities to support both professional 
biologist-level observation requirements as well as "simple" observations.

The enhanced iNaturalist system will replace the NZBRN's current 
observation platform, provide a new home for legacy observation data, 
and provide equivalent or better functionality with a much more modern 
interface (and with various web services interfaces to allow tight 
system-level integration with external systems, e.g. NZOR).

Dave

On 26/07/12 08:59, Andrew Watkins wrote:
> Do people envisage iNaturalist moving beyond 'simple' observations I.e
> species, time and place and into survey procedure based observations,
> including habitat measurements, more complex data entry forms etc?  Or
> will this remain the domain of domain specific systems?
>
>
> On 25/07/12 2:34 PM, "Colin Meurk" <MeurkC@landcareresearch.co.nz> wrote:
>
>> Also NZBRN (aka Nature Watch NZ) will be linked to NZOR.
>>
>> Picking up on a query yesterday on similarity of iSpot and iNaturalist
>> (the basis of Nature Watch NZ) I'd note that (based on a few months ago)
>> iSpot was basically a picture sharing system that u could get the
>> community to identify for you - the species in the pictures.  I think it
>> does map the locations of pictures, but it is not primarily set up to be
>> a biodiversity or biosecurity (distribution) database but rather a shared
>> identification tool.  However these things are morphing all the time!
>> iSpot is I think dependent on pictures whereas iNaturalist records
>> observations of species with or without attached pictures.  Perhaps they
>> can be characterised as an observation (spatio-temporal) versus a species
>> identification focus.
>> Cheers
>> c
>>
>> -----Original Message-----
>> From: dataversity_public_discuss@dataversity.org.nz
>> [mailto:dataversity_public_discuss@dataversity.org.nz] On Behalf Of Dan
>> Randow
>> Sent: Wednesday, 25 July 2012 2:12 p.m.
>> To: dataversity_public_discuss@dataversity.org.nz
>> Subject: [Dataversity] Integrated Biodiversity Management System
>>
>>
>> Jochen,
>>
>> I'll answer your question from "New Name for LRSS and IBMS"
>> <http://dataversity.org.nz/r/topic/5XpdgkZohD1XoOuxES1VFA> here. We don't
>> quite have a single system yet :).
>>
>>    can you tell us how you envisage that to
>>    integrate with NZOR and FBIS?
>>
>> Yes, integration with external system is a core requirement of IBMS with
>> NZOR, and national data systems such as FBIS and NVS all on the list.
>>
>> This is explained in sections 4.3 Interoperability Requirements and 4.4
>> Data Standards Compliance of the Scope
>> <http://dataversity.org.nz/r/file/33655-2012-07-19T003045Z>.
>>
>> Dan
>>
>> --
>> @danrandow +64-27-431-4928 +64-3-377-5377 Chief Wrangler,
>> http://dataversity.org.nz and http://onlinegroups.net
>>
>>
>> -----------------------------------------
>> Full text of this topic in Dataversity Public Discussion:
>> http://dataversity.org.nz/r/topic/6LrdUK0xdn75aTih8NWy2O
>>
>> To leave Dataversity Public Discussion, email
>> mailto:dataversity_public_discuss@dataversity.org.nz?Subject=unsubscribe
>>
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>> -----------------------------------------
>> Full text of this topic in Dataversity Public Discussion:
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>>
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    <entry>
      <title>iNaturalist</title>
      <link rel="alternate" type="text/html"
            title="iNaturalist"
            href="http://dataversity.org.nz/r/post/JLPMy15zsSo7UQEJng2aQ" />
      <id>http://dataversity.org.nz/r/post/JLPMy15zsSo7UQEJng2aQ</id>
      <author>
        <name>Dave Lane</name>
        <uri>/p/lightweight</uri>
      </author>
      <updated>2012-07-24T22:26:23Z</updated>
      <summary type="xhtml">
        <div xmlns="http://www.w3.org/1999/xhtml">
          Hello Andrew, Interesting to have that insight of NIWA software policies. It's worth pointing out that iNaturalist makes use of PostgreSQL as the underlying database for the main http://inaturalist.org and NZBRN deployments. Drupal, in general, uses MySQL (although PostgreSQL can be used,&#8230;
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          <pre>Hello Andrew,

Interesting to have that insight of NIWA software policies.

It's worth pointing out that iNaturalist makes use of PostgreSQL as the 
underlying database for the main http://inaturalist.org and NZBRN 
deployments. Drupal, in general, uses MySQL (although PostgreSQL can be 
used, but it creates occasional incompatibilities for the many modules 
which haven't been tested with PostgreSQL).

Also worth noting is that it's no secret that Symfony is a 
re-implementation of Ruby on Rails' concepts using PHP rather than Ruby. 
Symfony suits organisations who have lots of PHP expertise and/or lots 
of investment in PHP-specific infrastructure. That said, Ruby on Rails 
can be hosted on a very similar (fully open source) Linux server stack 
to PHP (even concurrently and harmoniously :) as on Egressive's 
infrastructure). A couple of our developers came to RoR by traversing 
from Drupal to Symfony and then on to RoR (mostly for the benefits 
inherent in the Ruby language, according to them). Many developers see 
learning a new programming language as a major impediment, others see it 
as no problem whatsoever, given that the concepts underlying them are 
all related.

I agree in the weight assessment you make. In Egressive's toolbox, Ruby 
on Rails is the middle-to-heavy weight complement to the light-to-middle 
weight Drupal (with a focus on Content Management Behaviour).

Kind regards,

Dave

On 25/07/12 09:42, Andrew Watkins wrote:
> The Systems Development team at NIWA use the following tools extensively:
>
> 1. Drupal - for content management only - NIWA and Riskscape websites etc.
>      - we prefer not to extend modules in CMSs as our experience is that
> content management systems - and websites generally have a different life
> cycle to the underlying data systems, middle ware and web services.
>
> 2. PHP on Symfony.  - for 3 Tier web systems (database, business rules,
> web user interface).
> E.g data entry forms, search tools some web services etc.
> This is the PHP equivalent of Ruby on Rails and borrows most of RORs
> concepts back into the more common programming language.  This is the most
> effective 'time to market' solution.
> Examples include the Environmental Information Browser ei.niwa.co.nz and
> the Taxonomic Attribute editor.
>
> 3. Java - for complex middleware, business rules, web services, thick
> client apps and persistent sessions.
> We use Java running under Tomcat or Jboss for more involved systems.
> E.g Taxon reference system TRS web services, NEMO web services etc.  and
> complex desktop applications such as RiskScape.
> Major tool chains such as Geonetwork (for metadata), GeoServer (for WMS,
> WFS etc) and upcoming SOS projects all use Java.
>
> We might think of these three layers as light, middle and heavyweight. To
> be chosen depending on the scale and life cycle of the project.
>
> Where database persistence is required we use Postgres/PostGIS for the
> most part, with some systems using the XML database eXist DB.
>
> Andrew
>
>
> On 25/07/12 9:09 AM, "Trent Bell" <trent@ecogecko.co.nz> wrote:
>
>> Absolutely helpful, Dave. This is the kind of advice I like to see more
>> often on here - very educational and illuminating, and based on
>> practical experience. If anyone else has nuggets like this, please share
>> with all.
>>
>> Trent Bell
>> EcoGecko Consultants
>> 32 Egmont St
>> New Plymouth
>> New Zealand
>> trent@ecogecko.co.nz
>> www.ecogecko.co.nz  <http://www.ecogecko.co.nz>
>> www.biogecko.co.nz  <http://www.biogecko.co.nz>
>> 027-284-7788 (SMS only)
>>
>> EcoGecko Consultants
>> On 24/07/2012 9:06 p.m., Dave Lane wrote:
>>> Hello Jerome,
>>>
>>> I can't provide a feature comparison as I've never used iSpot, but as  a
>>> director of Egressive, the software company developing the enhanced
>>> iNaturalist implementation for the NZBRN, I can tell you a bit about the
>>> underlying technologies on which both are built. The iNaturalist
>>> platform is built on the Ruby on Rails platform and iSpot is built on
>>> the Drupal platform. Egressive's two web development technologies happen
>>> to be Ruby on Rails and Drupal and we have used them commercially since
>>> 2008 and 2005 respectively.
>>>
>>> Both Ruby on Rails and Drupal are open source technologies and have
>>> massive developer communities. Both feature huge libraries of
>>> functionality - Drupal has thousands of themes and functional modules
>>> and Ruby on Rails features many hundreds of powerful "gems" (somewhat
>>> analogous to Drupal modules).
>>>
>>> Drupal is written in the ubiquitous PHP language (available on nearly
>>> every web host worldwide, considered commodity), and as such is easy for
>>> many developers to access and familiarise themselves with. The community
>>> welcomes beginners and represents a broad range of skill levels. Ruby on
>>> Rails is written in the Ruby language, which is a more advanced language
>>> than PHP, and its use requires a somewhat more advanced understanding of
>>> software concepts. Because of that, the community is somewhat smaller,
>>> but the typical technical level (and, therefore, the software quality
>>> standards) tends to be appreciably higher.
>>>
>>> Drupal is certainly a very powerful toolset, and has been used by a
>>> number of bio-diversity recording platforms. Because of its highly
>>> functional module collection, it allows developers to prototype the
>>> desired functionality very quickly. It is, however, primarily a content
>>> management system (CMS) and at some point the same highly structured
>>> module approach which allows a lot of functionality to be built very
>>> quickly transitions from being an enabler to becoming an impediment for
>>> refining that functionality. A number of the most ambitious
>>> bio-diversity platforms have developed to the point where wrestling with
>>> Drupal's in-built structure has largely halted progress. It seems a
>>> common path for these platforms (e.g. the Encyclopaedia of Life) to
>>> start with Drupal and achieve a certain level of capability. Then, when
>>> its developers reach those limits, they start again, adopting a more
>>> powerful platform. In the case of most who have outgrown Drupal (also
>>> e.g. the EoL), they move on to the Ruby on Rails platform. This same
>>> exact progression happens quite a lot in other software domains outside
>>> of bio-diversity recording as well.
>>>
>>> iNaturalist's technically superb (and highly proficient) original
>>> development team (in San Francisco) started the project using the Ruby
>>> on Rails platform, and in my professional opinion that choice makes it a
>>> substantially more robust and expansive application from a technology
>>> perspective, with greater scope for continuous improvement and advanced
>>> features. For example, we are now able to add NZBRN's functional
>>> requirements with relative ease on top of the very sound foundation
>>> they've created.
>>>
>>> For any on the list with software expertise, Ruby on Rails offers the
>>> technical advantages over Drupal of
>>> - by its design, facilitating test driven development allowing for more
>>> rigorous development processes
>>> - supporting continuous integration allowing a more robust deployment
>>> process (along with automated testing)
>>> - allow for much cleaner database schema than Drupal
>>> - making it easy to create powerful web services interfaces allowing
>>> external automated systems to interact with iNaturalist in very clever
>>> ways.
>>>
>>> So, while I can't comment on their relative current capabilities because
>>> I'm not familiar with iSpot, my experience with both underlying
>>> platforms makes me think that iNaturalist is a better target for further
>>> sector investment in software capabilities because it has far greater
>>> growth potential.
>>>
>>> Hope that's helpful.
>>>
>>> Kind regards,
>>>
>>> Dave
>>>
>>> On 24/07/12 19:49, Jerome Sullivan wrote:
>>>> Good day All,
>>>>
>>>> How does iNaturalist compare with iSpot?  Thank you.
>>>>
>>>> Kind regards,
>>>>
>>>> Jerome
>>>>
>>>> -----Original Message-----
>>>> From: dataversity_public_discuss@dataversity.org.nz
>>>> [mailto:dataversity_public_discuss@dataversity.org.nz] On Behalf Of Dan
>>>> Randow
>>>> Sent: 24 July 2012 04:55 AM
>>>> To: dataversity_public_discuss@dataversity.org.nz
>>>> Subject: [Dataversity] iNaturalist
>>>>
>>>>
>>>> iNaturalist <http://www.inaturalist.org/> is becoming established as a
>>>> significant player in the biodiversity data world. A new partnership
>>>> with the Encyclopedia of Life will see iNaturalist as the platform for
>>>> citizen-contributed observations to complement the species information
>>>> in EOL <http://eol.org/info/press_releases/info/June_18_2012>.
>>>>
>>>> iNaturalist is, of course the platform chosen by NZ Bio-recording
>>>> Network <http://dataversity.org.nz/r/topic/7tm89JFlymVR0v0SIJZWNE> as
>>>> its new platform for citizen science observations.
>>>>
>>>> Dan
>>>>
>>>> --
>>>> @danrandow +64-27-431-4928 +64-3-377-5377 Chief Wrangler,
>>>> http://dataversity.org.nz and http://onlinegroups.net
>>>>
>>>>
>>>> -----------------------------------------
>>>> Full text of this topic in Dataversity Public Discussion:
>>>> http://dataversity.org.nz/r/topic/4Jza3F933ttLQBPbkTCmnI
>>>>
>>>> To leave Dataversity Public Discussion, email
>>>>
>>>> mailto:dataversity_public_discuss@dataversity.org.nz?Subject=unsubscribe
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>>>> OnlineGroups.Net http://onlinegroups.net
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>>>>
>>>>
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>>>> HTTP://BIODIVERSITYADVISOR.SANBI.ORG/
>>>>
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>>
>>
>> -----------------------------------------
>> Full text of this topic in Dataversity Public Discussion:
>> http://dataversity.org.nz/r/topic/3RwrzMyK1FKtA1iz1roUJB
>>
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    <entry>
      <title>iNaturalist</title>
      <link rel="alternate" type="text/html"
            title="iNaturalist"
            href="http://dataversity.org.nz/r/post/TGU2ySYfaLmrjndw8RbAe" />
      <id>http://dataversity.org.nz/r/post/TGU2ySYfaLmrjndw8RbAe</id>
      <author>
        <name>Dave Lane</name>
        <uri>/p/lightweight</uri>
      </author>
      <updated>2012-07-24T09:06:55Z</updated>
      <summary type="xhtml">
        <div xmlns="http://www.w3.org/1999/xhtml">
          Hello Jerome, I can't provide a feature comparison as I've never used iSpot, but as a director of Egressive, the software company developing the enhanced iNaturalist implementation for the NZBRN, I can tell you a bit about the underlying technologies on which&#8230;
        </div>
      </summary>
      <content type="xhtml" xml:space="preserve">
        <div xmlns="http://www.w3.org/1999/xhtml">
          <pre>Hello Jerome,

I can't provide a feature comparison as I've never used iSpot, but as  a 
director of Egressive, the software company developing the enhanced 
iNaturalist implementation for the NZBRN, I can tell you a bit about the 
underlying technologies on which both are built. The iNaturalist 
platform is built on the Ruby on Rails platform and iSpot is built on 
the Drupal platform. Egressive's two web development technologies happen 
to be Ruby on Rails and Drupal and we have used them commercially since 
2008 and 2005 respectively.

Both Ruby on Rails and Drupal are open source technologies and have 
massive developer communities. Both feature huge libraries of 
functionality - Drupal has thousands of themes and functional modules 
and Ruby on Rails features many hundreds of powerful "gems" (somewhat 
analogous to Drupal modules).

Drupal is written in the ubiquitous PHP language (available on nearly 
every web host worldwide, considered commodity), and as such is easy for 
many developers to access and familiarise themselves with. The community 
welcomes beginners and represents a broad range of skill levels. Ruby on 
Rails is written in the Ruby language, which is a more advanced language 
than PHP, and its use requires a somewhat more advanced understanding of 
software concepts. Because of that, the community is somewhat smaller, 
but the typical technical level (and, therefore, the software quality 
standards) tends to be appreciably higher.

Drupal is certainly a very powerful toolset, and has been used by a 
number of bio-diversity recording platforms. Because of its highly 
functional module collection, it allows developers to prototype the 
desired functionality very quickly. It is, however, primarily a content 
management system (CMS) and at some point the same highly structured 
module approach which allows a lot of functionality to be built very 
quickly transitions from being an enabler to becoming an impediment for 
refining that functionality. A number of the most ambitious 
bio-diversity platforms have developed to the point where wrestling with 
Drupal's in-built structure has largely halted progress. It seems a 
common path for these platforms (e.g. the Encyclopaedia of Life) to 
start with Drupal and achieve a certain level of capability. Then, when 
its developers reach those limits, they start again, adopting a more 
powerful platform. In the case of most who have outgrown Drupal (also 
e.g. the EoL), they move on to the Ruby on Rails platform. This same 
exact progression happens quite a lot in other software domains outside 
of bio-diversity recording as well.

iNaturalist's technically superb (and highly proficient) original 
development team (in San Francisco) started the project using the Ruby 
on Rails platform, and in my professional opinion that choice makes it a 
substantially more robust and expansive application from a technology 
perspective, with greater scope for continuous improvement and advanced 
features. For example, we are now able to add NZBRN's functional 
requirements with relative ease on top of the very sound foundation 
they've created.

For any on the list with software expertise, Ruby on Rails offers the 
technical advantages over Drupal of
- by its design, facilitating test driven development allowing for more 
rigorous development processes
- supporting continuous integration allowing a more robust deployment 
process (along with automated testing)
- allow for much cleaner database schema than Drupal
- making it easy to create powerful web services interfaces allowing 
external automated systems to interact with iNaturalist in very clever ways.

So, while I can't comment on their relative current capabilities because 
I'm not familiar with iSpot, my experience with both underlying 
platforms makes me think that iNaturalist is a better target for further 
sector investment in software capabilities because it has far greater 
growth potential.

Hope that's helpful.

Kind regards,

Dave</pre>
        </div>
      </content>
    </entry>
  



    
    
  
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