Simons, James | 24 Jan 18:57 2015

FW: Afterthoughts . . . Re: gomexsi workshop wrap-up

Hi to all,

 

  I am forwarding the email concerning the recent GoMexSI/GloBI workshop.  I apologize to those who have already received the below email.

 

  Please feel free to communitcate with us if you have questions or are interested to know more about another workshop.

 

Thanks,

 

GoMexSI team

 

From: jorrit poelen [mailto:jhpoelen-qWit8jRvyhVmR6Xm/wNWPw@public.gmane.org]
Sent: Thursday, January 22, 2015 12:39 PM
To: Simons, James; Brian Hayden (brian.hayden-kQW2Dzt44JA@public.gmane.org); Yuan, May (myuan-DNmUmOh1Rg72fBVCVOL8/A@public.gmane.org); Dave Reed; Skyler Sagarese (s.sagarese1-6ft+5RaVQuW1zw4bZebV9Q@public.gmane.org); Jennifer Hammock; Bradley Ennis; rebeca.qp-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org; Kalen Rice; Mitchell, Theresa; Tracy Weatherall; Cai, Xiaopeng
Subject: Afterthoughts . . . Re: gomexsi workshop wrap-up

 

Hey y’all,

 

As you might know, we had a GloBI / GoMexSI workshop review session yesterday (Jan 21, 2015). You can find the notes here: https://github.com/GoMexSI/workshop/wiki/Post-workshop-Review .

 

One of the many take-aways I had is that folks are eager to learn more about GitHub and R for managing and accessing interaction data. I think the great thing about these tools is that a large community actively uses this tool combo to help with their scientific explorations, so many online resources are available. And . . . I am excited to see that the GoMexSI team is now actively using GitHub for data management (see https://github.com/gomexsi/interaction-data) and discussions (e.g. https://github.com/GoMexSI/interaction-data/issues/1). 

 

Here’s just two of the many R and GitHub introductions that are available online:

 

Hope this was useful and let me know if you have any questions,

-jorrit

 

PS Picture take during workshop at Texas A&M Corpus Christi in Dec 2014 (see https://github.com/GoMexSI/workshop/wiki/participants).

 

 

On Jan 17, 2015, at 2:41 PM, Simons, James <James.Simons-at6qt1C6Z5Y3uPMLIKxrzw@public.gmane.org> wrote:



Hi to all.

 

  Sorry for the short notice but we wanted to have a gomexsi post-workshop call for an hour or so this coming week on Wednesday, Jan 21st.  Please let us know if you are able/interested to attend.  We are thinking of doing it at 1300 Corpus time (CST).

 

  If this is too short of notice for most of you perhaps we can re-schedule, but it would have to be Feb 2,3 or 6.

 

Thanks,

 

Jim

 

 

James D. Simons, Ph.D.

Associate Research Scientist

 

Center for Coastal Studies

Natural Resources Center 3200

6300 Ocean Drive, Unit 5866

Corpus Christi, Texas 78412-5866

O 361.825.3223  *  F 361.825.2770

 

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Simons, James | 24 Jan 18:54 2015

GoMexSI update

Hi to all,

 

  I have been meaning to send this out for some time now.

 

  We currently have 62,759 lines of data from 103 references in the GoMexSI database, up from about 40K a short time ago.  In addition we have many thousands of lines of extracted data awaiting editing and mostly awaiting spatial data. We are working on both of these fronts now.

 

  Recently TAMUCC became a member of the Ecopath Consortium, in large part due to the efforts on the GoMecSI database and the leadership of Francisco Arreguin Sanchez who cited our work in a recent Fisheries Centre publication. I was able to attend the Ecopath 30 Years meeting in Barcelona and made some good contacts for the GoMexSI project.

 

  In early December we held a 2.5 day GoMexSI.GloBI workshop in which we discussed the database structure, use of R and Cypher to access data, and other topics.  I will forward a short email synopsis of the workshop wrap-up we held a couple of days ago.  We hope to have future workshops if there is interest.  Please let us know if you would like more info.

 

  We are busy with our MARFIN project and will soon be working on the gut contents of over 1000 fish specimens to add to the data collected by our collaborators at USF in Florida.

 

Thanks again to all of you for your interest and time.

 

The GoMexSI team,

 

 

James D. Simons, Ph.D.

Associate Research Scientist

 

Center for Coastal Studies

Natural Resources Center 3200

6300 Ocean Drive, Unit 5866

Corpus Christi, Texas 78412-5866

O 361.825.3223  *  F 361.825.2770

 

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Darren M Evans | 6 Jan 14:30 2015
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Funded PhD: ecological network robustness

Dear All

 

I have a funded PhD studying the robustness of ecological networks available in my lab. Would suit a numerate ecologist. Closing date is 2 Feb 2015. More details at: tinyurl.com/nrqu98b

 

Do forward this to anyone you know who might be interested.

 

Many thanks

 

Darren Evans

 

........................................................

 

Dr. Darren M. Evans

Senior Lecturer in Conservation Biology

 

School of Biological, Biomedical and Environmental Sciences

Room 317 Hardy Building

University of Hull

Cottingham Road

Hull

HU6 7RX

 

Website

Tel +44 (0)1482 465187

Twitter: <at> DarrenMarkEvans

 

..........................................................................

 

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Christian Mulder | 20 Nov 12:58 2014
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Novel soil food web in American Naturalist

Dear All

Please pass on to anyone you think might be interested.

Many thanks and regards

Christian


 


Dr. Christian Mulder
Quantitative Macroecology, head
Centre for Sustainability, Environment and Health
National Institute for Public Health and Environment
P.O.Box 1, NL-3720 BA Bilthoven, The Netherlands
https://www.researchgate.net/profile/Christian_Mulder2?ev=hdr_xprf
Phone Office: ++31 (0) 30 274 31 48 - Skype: christian.mulder.traitnet


Proclaimer RIVM http://www.rivm.nl/Proclaimer
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Darren M Evans | 24 Oct 18:46 2014
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BOU Day Conference ‘Advances in food-web theory and practice’, 19th November 2014, Peterborough, UK

There are a few places remaining at this fascinating conference that aims to: 1) bring together
ornithologists, entomologists, botanists and others studying species interactions across trophic
levels at all scales; 2) showcase new and emerging theory and practice in ecological networks to
stimulate further advances; and 3) highlight the applications of new molecular techniques to
understand food-webs.

We have an excellent programme of speakers, many of whom work in agro-ecosystems, including Pedro
Jordano, Jane Memmott, Bill Symondson, Gareth Jones, Anna Traveset and James Pearce-Higgins (see
http://www.bou.org.uk/conferences/foodwebs-speaker-abstracts.pdf) for full speaker list and abstracts.

Further details and booking can be found at http://www.bou.org.uk/conference/avian-food-webs/

Please consider attending or forwarding this email to those who you think would be interested.

Darren Evans

........................................................

Dr. Darren M. Evans
Senior Lecturer in Conservation Biology

School of Biological, Biomedical and Environmental Sciences
Room 317 Hardy Building
University of Hull
Cottingham Road
Hull
HU6 7RX

Website
Tel +44 (0)1482 465187
Twitter:  <at> DarrenMarkEvans

..........................................................................

BOU 2014 Autumn One-day Conference
BIRDS IN THE ENTANGLED BANK: ADVANCES IN FOODWEB THEORY AND PRACTICE
19th November 2014, Great Northern Hotel, Peterborough, UK http://www.bou.org.uk/conference/avian-food-webs/
...........................................................
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Simons, James | 18 Sep 20:49 2014

One year and 15 day update!!!

Hi to all,

 

  On September 3, 2013 we launched the GoMexSI database and webpage.  Since that time I believe I have provided one update.  I would like to provide another update as to where we stand at this point.  I would also like to thank all of those who have visited the website, and all of those who have contributed data.

 

  We have been extracting trophic data for over a year now.  We currently have 37,930 species interaction recorded in the database, from about 1500 unique interactors.  These come from 61 references and 6 contributed datasets. We also have an additional 22, 490 interactions that will be loaded in the next several months as we get the files edited and the spatial information taken care of. These data come from an additional 56 references, bringing the totals to 60,420 interactions and 117 references, which is 15.4% of the total of 758 references to fish trophic data we now have in hand.

 

  We are currently working to translate the webpage into Spanish, and hope to have that completed soon.

 

We are currently working under MARFIN and CIMAS grants to continue extracting and entering data, and will soon begin to collect and analyze new specimens for gut contents under the MARFIN grant.

 

  We have begun to complete the building of our lists of other taxa for trophic  data extraction, and have also collected a large list of references for parasites for the Gulf. See Table below for the current status of these taxa (which is always being updated).

 

Taxon

Group

Number of References Collected

Number of References Processed

Total Number of Species Currently Cited

Mammalia

Marine Mammals, Coastal Terrestrial Mammals

55

0

1

Reptilia

Sea Turtles, Coastal Terrestrial Reptiles

21

0

3

Actinopterygii

Estuarine and Marine Sharks, Rays and Fishes

758

61

646

Ares

Sea and Shore Birds

43

0

4

Arthropoda

Crustaceans and Insects

50

0

58

Mollusca

Estuarine and Marine Bivalves, Gastropods and Cephalopods

10

0

45

Annelida

Polychaete worms and Leeches

2

0

0

Echinodermata

Sea stars, Sea urchins, etc.

1

0

0

Ctenophora

Comb jellies

1

0

2

Cnidaria

Jellyfish, Box Jellies, Sea Wasps

5

0

6

Acanthocephala

Spiny Headed Worms

1

0

0

Platyhelminthes

Tapeworms and Flukes

60

0

0

Nematoda

Nematodes

4

0

0

Apicomplexa

Ciliated Protozoans, Hematozoans

4

0

0

Fungi

Fungi

3

0

0

Rhombozoa

Dicyemids

0

0

0

 

  I would like to announce an article that has been accepted for publication by Ecological Informatics titled “ Global Biotic Interactions: An open infrastructure to share and analyze species-interaction datasets “ by Jorrit Poelen, James Simons and Christopher Mungal.  Although not directly about GoMexSI, there is coverage of the GoMexSI database/webpage in the article.  Thanks to Jorrit for leading the effort on this endeavor.

 

  We are planning to present papers and/or posters at the upcoming GERS meeting at Port Aransas, TX, in October, and the Congreso Nacional de Ictiologia in Morelia, Mexico and hopefully the Ecopath Conference in Barcelona Spain, both in November.

 

Again, thanks to all who have had apart in making this database and webpage a success!!!

 

Take care,

 

Jim

 

PS  As always, if you would like to be removed from the email list, please let me know.

 

James D. Simons, Ph.D.

Associate Research Scientist

 

Center for Coastal Studies

Natural Resources Center 3200

6300 Ocean Drive, Unit 5866

Corpus Christi, Texas 78412-5866

O 361.825.3223  *  F 361.825.2770

 

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Darren M Evans | 16 Sep 16:31 2014
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BOU 2014 Autumn One-day Conference 19th November: Advances in foodweb theory and practice

Please consider attending the BOU Autumn One-day conference ‘Birds in the Entangled Bank: Advances in Foodweb Theory and Practice’ on the 19th November at the Great Northern Hotel, Peterborough, UK. I would be most grateful if you could also pass this information on to anyone you think might be interested. We have some excellent speakers (see the attached programme) and this will be great opportunity to hear from plant ecologists, entomologists, mammalogists and ornithologists all studying the complex ways in which species interact.  Full details can be found here:

 

http://www.bou.org.uk/conference/avian-food-webs/

 

Please note that early bird rates and reduced rates for BOU Early-career Researchers are available until 17 October.

 

I very much hope you can join us!

 

Darren Evans

 

PS apologies for cross-postings

 

........................................................

 

Dr. Darren M. Evans

Senior Lecturer in Conservation Biology

 

School of Biological, Biomedical and Environmental Sciences

Room 314A Hardy Building

University of Hull

Cottingham Road

Hull

HU6 7RX

 

Website

Tel +44 (0)1482 465187

Twitter: <at> DarrenMarkEvans

 

..........................................................................

 

Attachment (foodwebs-programme.pdf): application/pdf, 133 KiB
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Darren M Evans | 25 Jul 11:48 2014
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Lectureship in Ecology

Dear All

 

The University of Hull is currently recruiting for a 3-year Lectureship: https://jobs.hull.ac.uk/vacancy.aspx?ref=fs0124

 

I’m keen to encourage network ecologists to join our group http://www2.hull.ac.uk/science/bbes/research/ecologyandenvironment/networkecology.aspx

 

Do contact me for informal enquiries. Closing date is 26 August 2014.

 

Many thanks

 

Darren Evans

 

........................................................

 

Dr. Darren M. Evans

Senior Lecturer in Conservation Biology

 

School of Biological, Biomedical and Environmental Sciences

Room 314A Hardy Building

University of Hull

Cottingham Road

Hull

HU6 7RX

 

Website

Tel +44 (0)1482 465187

Twitter: <at> DarrenMarkEvans

 

..........................................................................

 

BOU 2014 Autumn One-day Conference

BIRDS IN THE ENTANGLED BANK: ADVANCES IN FOODWEB THEORY AND PRACTICE

19th November 2014, Great Northern Hotel, Peterborough, UK http://www.bou.org.uk/conference/avian-food-webs/

...........................................................

 

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Axel G. Rossberg | 22 Jul 23:00 2014
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Trophic niche-space imaging

Dear Colleagues,

Theoretical Ecology just published 

"Trophic niche-space imaging, using resource and consumer traits",
http://link.springer.com/article/10.1007%2Fs12080-014-0229-5

by Leo Nagelkerke and myself. 

A preprint can be found here:
http://axel.rossberg.net/paper/Nagelkerke2014TheoEcol_NicheSpaceImaging_preprint.pdf

In case you fancy trying some "nichespace photography" on your own,
here http://foodwebs.info/NagelkerkeRossberg2014-RCode.zip is a link
to R-code and data files that we used, since for some reason they did
not make it onto the journal page, yet.

Please feel free to contact me or Leo with any comments or questions.

Best wishes,
Axel

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Abstract:

The strength of trophic (feeding) links between two species depends on
the traits of both the consumer and the resource. But which traits of
consumer and resource have to be measured to predict link strengths,
and how many? A novel theoretical framework for systematically
determining trophic traits from empirical data was recently
proposed. Here we demonstrate this approach for a group of 14 consumer
fish species (Labeobarbus spp., Cyprinidae) and 11 aquatic resource
categories coexisting in Lake Tana in northern Ethiopia, analysing
large sets of phenotypic consumer and resource traits with known roles
in feeding ecology. We systematically reconstruct structure and
geometry of trophic niche space, in which link strengths are predicted
by the distances between consumers and resources. These distances are
then represented graphically resulting in an image of trophic niche
space and its occupancy. We find trophic niche to be
multi-dimensional. Among the models we analysed, one with two resource
and two consumer traits had the highest predictive power for link
strength.  Results further suggest that trophic niche space has a
pseudo-Euclidean geometry, meaning that link strength decays with
distance in some dimensions of trophic niche space, while it increases
with distance in other dimensions. Our analysis not only informs
theory and modelling, but may also be helpful for predicting trophic
link strengths for pairs of other, similar species.
Ursula Gaedke | 27 May 16:15 2014
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Post Doc position Theoretical Community Ecology

Dear collaegues,

I am happy to announce the following position (also attached) and look forward to suitable applications:

Post-Doc Position in Theoretical Community Ecology at Potsdam, Germany

Pending final approval of funding we offer a full time position for 3 years with a potential second funding period of 3 more years at the department of Ecology/Ecosystem Modelling at Potsdam University (German salary scale E 13, 100%). The position is available within the recently established Priority Programme “Flexibility matters: Interplay between trait diversity and ecological dynamics using aquatic communities as model systems” (www.DynaTrait.de) funded by the German Science Foundation (DFG). We are seeking a highly motivated and productive scientist who is interested and capable of contributing to a modelling team closely interacting with experimentalists conducting laboratory food web experiments. She/he should have strong research interests in community and trait-based ecology (e.g. dynamics of predator-prey and multi-trophic systems), and in the role of adaptability for system dynamics in particular (e.g. via eco-evolutionary dynamics). The work includes developing and analyzing predator-prey and food web models which account for ongoing mutual adaptations of trait values among interacting organisms related to corresponding experiments.
The ideal candidate holds a Ph.D., has an excellent publication record in the field of theoretical ecology and ecological modelling and comprehensive skills in working with systems of differential equations. Prior Post-Doc experience, skills in time-series analysis and interest in co-supervising students is highly welcome. The modelling team, consisting of Post-Docs, Ph.D. and Master students, is supervised by Prof. Dr. Ursula Gaedke and Prof. Dr. Horst Malchow (Univ. Osnabrück) and provides a very stimulating research environment for promoting theoretical ecology by modelling and empirical studies. The position may be suitable to strive for a Habilitation. Fluency in English is essential but gaining some control of the German language is expected. Potsdam (near Berlin, Germany) is an attractive town of about 170,000 inhabitants.  It is an UNESCO world heritage and due to its close vicinity to Berlin covers a broad spectrum of all kinds of cultural activities.
For further information please visit http://www.uni-potsdam.de/en/ibb/researchgroups/ fullprofessors/ecology-and-ecosystem-modelling.html or contact U. Gaedke (gaedke <at> uni-potsdam. de). Applications should include a statement of motivation, a detailed CV with the list of publications, contact details of academic referees and degree certificates. Please send them electronically, if possible as a single file, to U. Gaedke. The position is open until it gets filled. The “12-years-rule” does not apply for this position.


Ursula Gaedke


Ökologie & Ökosystemmodellierung        Dept. Ecology & Ecosystem Modeling
Universität Potsdam                     University of Potsdam
Institut für Biochemie und Biologie     Institute of Biochemistry and Biology
Maulbeerallee 2

Postal address:
Am Neuen Palais 10
D-14469 Potsdam, Germany

Tel.    + 49 (0)331-977-1900/1902
Fax     + 49 (0)331-977-1948
e-mail Gaedke-KiJTPfjSHVUubQSw3dWLiw@public.gmane.org

http://www.uni-potsdam.de/en/ibb/researchgroups/fullprofessors/ecology-and-ecosystem-modelling.html

http://www.bio.uni-potsdam.de/professuren/oekosystemmodellierung

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Axel G. Rossberg | 23 Feb 00:53 2014
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SIZEWEB just appeared in the February issue of Ecology

... forwarding from Christian Mulder ...
 <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at> 

Dear Colleagues,

I am happy to announce the launch of the free-downloadable SIZEWEB database
(the acronym refers to Soil Invertebrates and Zoocoenoses in Edaphic Webs).
Please pass along this announcement to others you feel may have an interest in
SIZEWEB.
The entire database has been posted at http://esapubs.org/archive/ecol/E095/
051/ and on my ResearchGate profile.

All the best, Christian

(sorry for cross-posting)

 Soil invertebrates, chemistry, weather, human management, and edaphic food          
 webs at 135 sites in The Netherlands: SIZEWEB                                       
 Joel E. Cohen and Christian Mulder                                                  
 Ecology, Vol. 95, No. 2, February 2014.                                             
 Abstract | PDF (58 KB)                                                              

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