<div dir="ltr"><div><div>Nils,<br><br></div>Really great... 🙂 Thanks for sharing!<br><br></div>Salud!<br></div><div class="gmail_extra"><br><div class="gmail_quote">2016-06-01 6:09 GMT-03:00 Nils Hempelmann <span dir="ltr"><<a href="mailto:info@nilshempelmann.de" target="_blank">info@nilshempelmann.de</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
Hi Juan et al <br>
<br>
Thanks a lot for triggering this discussion. <br>
I am currently working on a Web processing service
(<a href="http://birdhouse.readthedocs.io/en/latest/" target="_blank">http://birdhouse.readthedocs.io/en/latest/</a>) including a species
distribution model based on the GBIF data (and climate model data).
A good connection to GBIF database is still missing and all hints
were quite useful!!<br>
<br>
If you want to share code:<br>
<a href="https://github.com/bird-house/flyingpigeon/blob/master/flyingpigeon/processes/wps_sdm.py" target="_blank">https://github.com/bird-house/flyingpigeon/blob/master/flyingpigeon/processes/wps_sdm.py</a>
<br>
<br>
Merci<br>
Nils <br>
<br>
<div>On 31/05/2016 22:08, Juan M. Escamilla
Molgora wrote:<br>
</div>
<blockquote type="cite">
<p>Hi Tim,</p>
<p>Thank you! specially for the DwC-A hint.</p>
<p>The cells are by default in decimal degrees, (wgs84 ) but the
functions for generating them are general enough to use any
projection supported by gdal using postgis. It could be done "on
the fly" or stored on the server side,</p>
<p>I was thinking (day dreaming) in a standard way for coding
unique but universal grids (similar to geohash or open location
code), but didn't find something fast and ready. Maybe later :)
<br>
</p>
<p>I only use Open Source Software, Python, Django, GDAL, Numpy,
Postgis, Conda, Py2Neo, ete2 among others.</p>
<p>Currently I don't have an official release and the project is
quite inmature, unstable as well as the installation could be
non trivial. I'm fixing all these issues but will take some
time,sorry for this.<br>
</p>
<p>The github repository is:<br>
</p>
<p><a href="https://github.com/molgor/biospytial.git" target="_blank">https://github.com/molgor/biospytial.git</a></p>
<p>An there's a very old documentation here: <br>
</p>
<p><a href="http://test.holobio.me/modules/gbif_taxonomy_class.html" target="_blank">http://test.holobio.me/modules/gbif_taxonomy_class.html</a><br>
</p>
<p>Please feel free to follow!<br>
</p>
<p><br>
</p>
<p>Best wishes</p>
<p><br>
</p>
<p>Juan<br>
</p>
<p>P.s. The functions for generating the grid are in:
biospytial/SQL_functions</p>
<p><br>
</p>
<p><br>
</p>
<p><br>
</p>
<br>
<div>On 31/05/16 19:47, Tim Robertson
wrote:<br>
</div>
<blockquote type="cite">
<div>Thanks Juan</div>
<div><br>
</div>
<div>You're quite right - you need the
DwC-A download format to get those IDs. </div>
<div><br>
</div>
<div>Are the cells decimal degrees, and
then partitioned into smaller units, or equal area cells or
maybe UTM grids or something else perhaps? I am just curious.</div>
<div><br>
</div>
<div>Are you developing this as OSS? I'd
like to follow progress if possible?</div>
<div><br>
</div>
<div>Thanks,<br>
<div>Tim,</div>
</div>
<div><br>
On 31 May 2016, at 20:31, Juan M. Escamilla Molgora <<a href="mailto:j.escamillamolgora@lancaster.ac.uk" target="_blank"></a><a href="mailto:j.escamillamolgora@lancaster.ac.uk" target="_blank">j.escamillamolgora@lancaster.ac.uk</a>>
wrote:<br>
<br>
</div>
<blockquote type="cite">
<div>
<p>Hi Tim, <br>
</p>
<p>The grid is made by selecting a square area and divide it
in nxn subsquares which form a partition on the bigger
square.</p>
<p>Each grid is a table in postgis and there's a mapping
between this table to a django model (class).</p>
<p>The class constructor have attributes: id, cell and
neighbours (next release).</p>
<p>The cell is a polygon (square) and with geodjango
inherits the properties of the osgeo module for polygons.
<br>
</p>
<p>I've tried to use the CSV data (downloaded as a CSV
request ) but I couldn't find a way to obtain the global
id's for each taxonomic level (idspecies, idgenus,
idfamily, etc).</p>
<p>Do you know a way for obtaining these fields?</p>
<p><br>
</p>
<p>Thank you for your email and best wishes,</p>
<p><br>
</p>
<p>Juan<br>
</p>
<br>
<div>On 31/05/16 19:03, Tim
Robertson wrote:<br>
</div>
<blockquote type="cite">
<div>Hi Juan</div>
<div><br>
</div>
<div>That sounds like a fun
project!</div>
<div><br>
</div>
<div>Can you please describe your
grid / cells? </div>
<div><br>
</div>
<div>Most likely your best bet
will be to use the download API (as CSV data) and ingest
that. The other APIs will likely hit limits (e.g. You
can't page through indefinitely).<br>
<br>
Thanks,<br>
<div>Tim</div>
</div>
<div><br>
On 31 May 2016, at 18:55, Juan M. Escamilla Molgora <<a href="mailto:j.escamillamolgora@lancaster.ac.uk" target="_blank"></a><a href="mailto:j.escamillamolgora@lancaster.ac.uk" target="_blank">j.escamillamolgora@lancaster.ac.uk</a>>
wrote:<br>
<br>
</div>
<blockquote type="cite">
<div>
<p>Dear all,</p>
<p><br>
</p>
<p>Thank you very much for your valuable feedback!</p>
<p><br>
</p>
<p>I'll explain a bit what I'm doing just to clarify,
sorry if this spam to some.</p>
<p><br>
</p>
<p>I want to build a model for species assemblages
based on co-occurrence of taxa within an arbitrary
area. I'm building a 2D lattice in which for each
cell I'm collapsing the data into a taxonomic tree
(the occurrences). For doing this I need first to
obtain the data from the gbif api and later, based
on the ids (or names) of each taxonomic level (from
kingdom to occurrence) build a tree coupled to each
cell. <br>
</p>
<p><br>
</p>
<p>The implementation is done with postgresql
(postgis) for storing the raw gbif data and neo4j
for storing the relation <br>
</p>
<p>"Being a member of the [ specie, genus, family,,,]
[name/id]" The idea is to include data from
different sources similar to the project Matthew and
Jennifer had mentioned (which I'm very interested
and like to hear more) and traverse the network
looking for significant merged information. <br>
</p>
<p><br>
</p>
<p>One of the immediate problems I've found is to
import big chunks of the gbif data into my
specification. Thanks to this thread I've found the
tools that are the most used by the community
(pygbif,rgbif, and python-dwca-reader). I was using
urlib2 and things like that. <br>
</p>
<p>I'll be happy to share any code or ideas with the
people interested.</p>
<p><br>
</p>
<p>Btw, I've checked the tinkerpop project which uses
the Gremlin traversal language as independent from
the DBMS. <br>
</p>
<p>Perhaps it's possible to use it with spark and
Guoda as well?</p>
<p><br>
</p>
<p><br>
</p>
<p>Does GOuda is working now?</p>
<p><br>
</p>
<p>Best wishes</p>
<p><br>
</p>
<p>Juan.<br>
</p>
<p><br>
</p>
<p><br>
</p>
<p><br>
</p>
<p><br>
</p>
<p><br>
</p>
<br>
<div>On 31/05/16 17:02,
Collins, Matthew wrote:<br>
</div>
<blockquote type="cite">
<p>Jorrit pointed out this thread to us at iDigBio.
Downloading and importing data into a relational
database will work great, especially if as Jan
said you can cut the data size down to a
reasonable amount.<br>
</p>
<p><span style="font-size:12pt"><br>
</span></p>
<p><span style="font-size:12pt">Another approach
we've been working on in a collaboration called
GUODA [1] is to build an Apache Spark
environment with pre-formatted data frames with
common data sets in them for researchers to use.
This approach would offer a remote service where
you could write arbitrary Spark code,
probably in Jupyter notebooks, to iterate over
data. Spark does a lot of cool stuff including
GraphX which might be of interest. This is </span>definitely
pre-alpha at this point and if anyone is
interested, I'd like to hear your thoughts.<span style="font-size:12pt"> I'll also be at SPNHC
talking about this.</span></p>
<p><span style="font-size:12pt"><br>
</span></p>
<p>One thing we've found in working on this is that
importing data into a structured data format isn't
always easy. If you only want a few columns,
it'll be fine. But getting the data typing, format
standardization, and column name syntax of the
whole width of an iDigBio record right requires
some code. <span style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:16px;background-color:rgb(255,255,255)"> I looked
to see if </span><span style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:16px;background-color:rgb(255,255,255)">EcoData R</span><span style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:16px;background-color:rgb(255,255,255)">etriever [2] had a GBIF data source and
they have an eBird o</span><span style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:16px;background-color:rgb(255,255,255)">ne that perhaps you might
find useful as a</span> starting point if you
wanted to try to use someone else's code to
download and import data.<br>
</p>
<p><br>
</p>
<p>For other data structures like BHL, we're kind of
making stuff up since we're packaging a relational
structure and not something nearly as flat as GBIF
and DWC stuff. <br>
</p>
<p><br>
</p>
<p>[1] <a href="http://guoda.bio/" target="_blank">http://guoda.bio/</a><br>
</p>
<p>[2] <a href="http://www.ecodataretriever.org/" target="_blank">http://www.ecodataretriever.org/</a><br>
</p>
<p><br>
</p>
<div>
<div name="divtagdefaultwrapper">
<div style="font-family:Tahoma;font-size:13px">
<div style="font-family:Tahoma;font-size:13px">Matthew Collins<br>
Technical Operations Manager<br>
Advanced Computing and Information Systems
Lab, ECE<br>
University of Florida<br>
<span><a href="callto:352-392-5414" target="_blank">352-392-5414</a></span></div>
</div>
</div>
</div>
<div style="word-wrap:break-word">
<hr style="display:inline-block;width:98%">
<div dir="ltr"><font style="font-size:11pt" color="#000000" face="Calibri, sans-serif"><b>From:</b> jorrit
poelen <a href="mailto:jhpoelen@xs4all.nl" target="_blank">
<jhpoelen@xs4all.nl></a><br>
<b>Sent:</b> Monday, May 30, 2016 11:16 AM<br>
<b>To:</b> Collins, Matthew; Thompson,
Alexander M; Hammock, Jennifer<br>
<b>Subject:</b> Fwd: [API-users] Is there any
NEO4J or graph-based driver for this API ?</font>
<div> </div>
</div>
<div>Hey y’all:
<div><br>
</div>
<div>Interesting request below on the
GBIF mailing list - sounds like a perfect fit
for the GUODA use cases. </div>
<div><br>
</div>
<div>Would it be too early to jump onto
this thread and share our efforts/vision?</div>
<div><br>
</div>
<div>thx,<br>
</div>
<div>-jorrit<br>
<div><br>
<blockquote type="cite">
<div>Begin forwarded message:</div>
<br>
<div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px"> <span><b>From: </b></span><span>Jan Legind <<a href="mailto:jlegind@gbif.org" target="_blank"></a><a href="mailto:jlegind@gbif.org" target="_blank">jlegind@gbif.org</a>><br>
</span></div>
<div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px"> <span><b>Subject: </b></span><span><b>Re:
[API-users] Is there any NEO4J or
graph-based driver for this API ?</b><br>
</span></div>
<div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px"> <span><b>Date: </b></span><span>May 30, 2016 at
5:48:51 AM PDT<br>
</span></div>
<div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px"> <span><b>To: </b></span><span>Mauro Cavalcanti
<<a href="mailto:maurobio@gmail.com" target="_blank">maurobio@gmail.com</a>>,
"Juan M. Escamilla Molgora" <<a href="mailto:j.escamillamolgora@lancaster.ac.uk" target="_blank"></a><a href="mailto:j.escamillamolgora@lancaster.ac.uk" target="_blank">j.escamillamolgora@lancaster.ac.uk</a>><br>
</span></div>
<div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px"> <span><b>Cc: </b></span><span>"<a href="mailto:api-users@lists.gbif.org" target="_blank">api-users@lists.gbif.org</a>"
<<a href="mailto:api-users@lists.gbif.org" target="_blank">api-users@lists.gbif.org</a>><br>
</span></div>
<br>
<div>
<div style="font-family:Helvetica;font-size:12px;font-style:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
<span style="font-family:Calibri,sans-serif;color:rgb(31,73,125)">Dear Juan,</span></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
<span style="font-family:Calibri,sans-serif;color:rgb(31,73,125)"> </span></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
<span style="font-family:Calibri,sans-serif;color:rgb(31,73,125)">Unfortunately
we have no tool for creating these
kind of SQL like queries to the
portal. I am sure you are aware
that the filters in the occurrence
search pages can be applied in
combination in numerous ways. The
API can go even further in this
regard[1], but it not well suited
for retrieving occurrence records
since there is a 200.000 records
ceiling making it unfit for
species exceeding this number.</span></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
<span style="font-family:Calibri,sans-serif;color:rgb(31,73,125)"> </span></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
<span style="font-family:Calibri,sans-serif;color:rgb(31,73,125)">There is
going be updates to the pygbif
package[2] in the near future that
will enable you to launch user
downloads programmatically where a
whole list of different species
can be used as a query parameter
as well as adding polygons.[3]</span></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
<span style="font-family:Calibri,sans-serif;color:rgb(31,73,125)"> </span></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
<span style="font-family:Calibri,sans-serif;color:rgb(31,73,125)">In the
meantime, Mauro’s suggestion is
excellent. If you can narrow your
search down until it returns a
manageable download (say less than
100 million records), importing
this into a database should be
doable. From there, you can refine
using SQL queries.</span></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
<span style="font-family:Calibri,sans-serif;color:rgb(31,73,125)"> </span></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
<span style="font-family:Calibri,sans-serif;color:rgb(31,73,125)">Best,</span></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
<span style="font-family:Calibri,sans-serif;color:rgb(31,73,125)">Jan K.
Legind, GBIF Data manager </span></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
<span style="font-family:Calibri,sans-serif;color:rgb(31,73,125)"> </span></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
<span style="font-family:Calibri,sans-serif;color:rgb(31,73,125)">[1]<span> </span><a href="http://www.gbif.org/developer/occurrence#search" target="_blank"></a><a href="http://www.gbif.org/developer/occurrence#search" target="_blank">http://www.gbif.org/developer/occurrence#search</a></span></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
<span style="font-family:Calibri,sans-serif;color:rgb(31,73,125)">[2]<span> </span><a href="https://github.com/sckott/pygbif" target="_blank"></a><a href="https://github.com/sckott/pygbif" target="_blank">https://github.com/sckott/pygbif</a></span></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
<span style="font-family:Calibri,sans-serif;color:rgb(31,73,125)">[3]<span> </span><a href="https://github.com/jlegind/GBIF-downloads" target="_blank"></a><a href="https://github.com/jlegind/GBIF-downloads" target="_blank">https://github.com/jlegind/GBIF-downloads</a></span></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
<span style="font-family:Calibri,sans-serif;color:rgb(31,73,125)"> </span></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
<b><span style="font-size:10pt;font-family:Tahoma,sans-serif">From:</span></b><span style="font-size:10pt;font-family:Tahoma,sans-serif"><span> </span>API-users
[<a href="mailto:api-users-bounces@lists.gbif.org" style="color:purple;text-decoration:underline" target="_blank">mailto:api-users-bounces@lists.gbif.org</a>]<span> </span><b>On Behalf Of<span> </span></b>Mauro
Cavalcanti<br>
<b>Sent:</b><span> </span>30.
maj 2016 14:06<br>
<b>To:</b><span> </span>Juan
M. Escamilla Molgora<br>
<b>Cc:</b><span> </span><a href="mailto:api-users@lists.gbif.org" target="_blank"></a><a href="mailto:api-users@lists.gbif.org" target="_blank">api-users@lists.gbif.org</a><br>
<b>Subject:</b><span> </span>Re:
[API-users] Is there any NEO4J or
graph-based driver for this API ?</span></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
</div>
<div>
<div>
<div>
<p class="MsoNormal"> Hi,</p>
</div>
<p class="MsoNormal"> One solution I
have successfully adopted for
this is to download the records
(either "manually" via browser
or, yet better, using a Python
script using the fine pygbif
library), storing them into a
MySQL or SQLite database and
then perform the relational
queries. I can provide examples
if you are interested.</p>
</div>
<div> Best regards,</div>
</div>
<div>
<div> </div>
<div>
<div> 2016-05-30 8:59
GMT-03:00 Juan M. Escamilla
Molgora <<a href="mailto:j.escamillamolgora@lancaster.ac.uk" target="_blank"></a><a href="mailto:j.escamillamolgora@lancaster.ac.uk" target="_blank">j.escamillamolgora@lancaster.ac.uk</a>>:</div>
<div> Hola,<br>
<br>
Is there any API for making
relational queries like
taxonomy, location or timestamp?<br>
<br>
Thank you and best wishes<br>
<br>
Juan<br>
_______________________________________________<br>
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</div>
<div> <br>
<br clear="all">
<br>
--<span> </span></div>
<div>
<div> Dr. Mauro J.
Cavalcanti<br>
E-mail:<span> </span><a href="mailto:maurobio@gmail.com" target="_blank"></a><a href="mailto:maurobio@gmail.com" target="_blank">maurobio@gmail.com</a><br>
Web:<span> </span><a href="http://sites.google.com/site/maurobio" target="_blank"></a><a href="http://sites.google.com/site/maurobio" target="_blank">http://sites.google.com/site/maurobio</a></div>
</div>
</div>
</div>
<span style="font-family:Helvetica;font-size:12px;font-style:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important">_______________________________________________</span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
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</blockquote>
</div>
<br>
</div>
</div>
</div>
<br>
<fieldset></fieldset>
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<pre>_______________________________________________
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<br></blockquote></div><br><br clear="all"><br>-- <br><div class="gmail_signature" data-smartmail="gmail_signature">Dr. Mauro J. Cavalcanti<br>E-mail: <a href="mailto:maurobio@gmail.com" target="_blank">maurobio@gmail.com</a><br>Web: <a href="http://sites.google.com/site/maurobio" target="_blank">http://sites.google.com/site/maurobio</a></div>
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