“GEOMETRIC MORPHOMETRICS IN R “. Del 26 al 30 de enero, 2015; 35 horas presenciales. Profesor: Dr. JULIEN CLAUDE (Institut des Sciences de l’Évolution de Montpellier, Francia).

Transmitting Science ha abierto la inscripción de un nuevo curso que puede ser de interés para miembros de esta lista:

– “GEOMETRIC MORPHOMETRICS IN R “. Del 26 al 30 de enero, 2015; 35 horas presenciales. Profesor: Dr. JULIEN CLAUDE (Institut des Sciences de l’Évolution de Montpellier, Francia).

Página web del curso: http://www.transmittingscience.org/courses/gm/gm-in-r/

PROGRAMA (el curso será en inglés):
1. An Introduction to R / Image Processing / Organizing Morphometric Data.
– Some Basics in R: The R Environment. R objects, Assigning, Indexing. Generating Data in R. 2D and 3D Plots in R; Interacting with the Graphs.
– Organizing Data for Morphometrics: Data-frame, Array and List. Converting and Coercing Objects. Read and Write Morphometric Data in R.
– Image Processing in R: Reading Various Image Files. Obtaining Image Properties. Modifying Image Properties: Contrast, Channels, Saturation Directly from R or by Interfacing R with Imagemagick.
– Simple Tests, Simple Linear Modelling, Alternatives to Linear Modeling, an example using traditional morphometrics. Defining size and shape using PCA and log-shape ratio approaches. Getting stats and test outputs. Testing assumptions of linear modeling. Testing for allometry and isometry. Solutions when assumptions of linear modeling are not met.
2. Landmark data.
– Acquiring Landmark Data in R.
– Plotting Landmark Configurations in 2 and in 3D: Using Different Symbols and Setting the Graphical Parameters. Labeling Landmarks.
– Geometric Transformation with Landmark Configurations: Translation. Scaling using Baseline or Centroid Size. Rotation.
– Superimposing and Comparing Two Shapes: 2.4.1. Baseline Superimposition. Ordinary Least Squares Superimposition. Resistant Fit.
– Representing Shape Differences: Plotting Superimposed Shape with Wireframe. Lollipop Diagrams and Vector Fields. Thin Plate Splines and Warped Shapes.
– Superimposing More Than Two Shapes. Baseline Registration. Full Generalized Procrustes Analysis. Partial Generalized Procrustes Analysis. Dimensionality of Superimposed Coordinates.
– Exploring Shape Variation and Testing Hypotheses: PCA. Multivariate Linear Modeling (Multivariate Regression and MANOVA). Allometry free approaches (Burnaby correction). Linear discriminant and Canonical Analysis.
3. Outlines.
– Acquiring outline Data in R: Fourier Analysis. Principles. Fourier Analysis of the Tangent Angle. Radius Fourier Analysis. Elliptic Fourier Analysis. Reduction of Shape Variables. Statistical Analysis of Shape Variation with Fourier Analysis. Exploring Shape Variation and Testing Hypotheses. PCA. Multivariate Linear Modeling (Multivariate Regression and MANOVA). Canonical Analysis.
– Combining Landmarks and Curves: Hybrid Methods between Fourier and Procrustes Analysis. Sliding Semi Landmarks.
– Solutions for Open Curves
4. Specific Applications.
– Testing Measurement Error.
– Partitional Clustering: K-means, Partition Around Medoids. Mclust. Combining Genetic, Geographic and Morphometric Data.
– Modularity / Integration Studies: Two-block Partial Least Squares. Testing Among Various Sets of Modules. Fluctuating Asymmetry and Directional Asymmetry. Inter-Individual and Intra-Individual Variation. Object and Matching Symmetry.
– Phylogenetic Data: The Problem of Phylogenetic Non-independence. Plotting the Tree in the Shape Space, Testing Evolutionary Models, Estimating Ancestral Character States. Morphological Disparity Through Time Diagram.
– Bending Energy, Uniform and Non-uniform Shape Variation.
Lugar: Centre de Restauració i Interpretació Paleontologica, Els Hostalets de Pierola, Barcelona (Spain).

Organizado por: Transmitting Science, el Institut Catalá de Paleontologia Miquel Crusafont y el Centre of Restauració i Interpretació Paleontologica.

Un cordial saludo

Soledad De Esteban Trivigno, PhD.
Directora del curso
Transmitting Science


NOAA Climate and Global Change Postdoctoral

University Corporation for Atmospheric Research – EUA

Application deadline: 9 January 2015

The UCAR Visiting Scientist Programs announces the 2015 recruitment for NOAA Climate and Global Change Postdoctoral Fellowships (C&GC). The fellowship program has an outstanding reputation of attracting the best and the brightest PhDs in the sciences relevant to the NOAA Climate and Global Change Program. Appointed fellows are hosted by a mentoring scientist at U.S. universities and research institutions to work in an area of mutual interest.

NOAA Climate and Global Change Postdoctoral Fellows focus on observing understanding, modeling, and predicting climate variability and change on seasonal and longer time scales. This includes the documentation and analysis of past, current, or possible future climate variability and change and the study of the underlying physical, chemical, and biological processes.

Applications are due 9 January. Appointments will be announced in March 2015.

Preference is given to those who have held a PhD for no more than three years. Awardees must change institutions and identify a host, who must be at a U.S. institution. A clearly articulated research proposal is particularly important. A steering committee, broadly representing the areas covered by this program, selects the fellows. The selection criteria used by the steering committee in making the awards is available at www.vsp.ucar.edu/cgc.

Advanced contact with a potential host is required. Interested host scientists are required to submit a brief letter of intent to host the fellow and a curriculum vita. Hosts are expected to mentor the fellow and cover office, computing, laboratory, and field research needs of the fellow as appropriate.

C&GC fellows are UCAR employees and receive a fixed annual salary plus UCAR’s benefits (health and dental insurance, paid time off, paid holidays, TIAA/CREF retirement fund, and life insurance). Allowances are provided for relocation and scientific travel during the appointment. Some funds may be available to support the cost of publications.

For additional information on this program and instructions on how to apply, please visit: www.vsp.ucar.edu/cgc. For further information, call (303) 497-1605 or e-mail vspapply@ ucar.edu.

The NOAA Climate Program Office sponsors this program. The University Corporation for Atmospheric Research is an EO/AAE who encourages and values diversity in the workplace.

(publicado em http://www.earthworks-jobs.com a 06-10-14)

[Se desejar manter-se informado sobre as oportunidades de emprego que surgem diariamente na área do Ambiente e Gestão de Recursos Naturais, siga a página “NaturJobs” que a Naturlink criou no Facebook em http://facebook.com/NaturJobs e no Twitter em http://twitter.com/NaturJobs]



Sharing knowledge to protect our marine environment

The JRC has set up the MSFD Competence Centre (MCC) to help EU countries achieve ‘Good Environmental Status’ of their marine waters by 2020, the main aim of the Marine Strategy Framework Directive (MSFD). In achieving this aim, the MSFD seeks to protect the fragile balance of marine ecosystems, upon which many economic and social activities such as fishing or tourism depend.

The MCC acts as a science-policy interface, facilitating cooperation and information exchange for the successful implementation of the Directive.

The MCC constitutes a platform on which to share knowledge and scientific expertise on methods and modelling tools, and provides access to guidance, assessments and reviews. It is the result of a close collaboration between the European Commission, the European Environment Agency, EU Member States, Regional Sea Conventions (RSCs), the International Council for the Exploration of the Sea (ICES) and the European research community.

The MCC will act as a single entry point for policy-review activities, including the current review of the criteria and methodological standards for good environmental standards, which are key to achieving the MSFD goal. It will also provide useful modelling tools for the assessment of MSFD descriptors and serve as a knowledge broker, bridging the science-policy divide by feeding the implementation and adaptation process with relevant knowledge from the scientific community. The MCC has a web interface that brings together relevant tools and information, including assessment approaches, methodological standards or links to other related initiatives, such as the European Marine Observation and Data network (EMODnet).

Launch at the EurOCEAN 2014 conference

The new MSFD Competence Centre was launched today by JRC Director for Environment and Sustainability, Maria Betti, at the EurOCEAN 2014 conference in Rome. This conference brings together marine scientists from across the broad range of disciplines, policymakers, and representatives of industry and NGOs, to develop a common vision for achieving an ecosystem approach to the management of Europe’s marine resources, a fundamental requirement for sustainable Blue Growth.


European seas and oceans provide benefits that can be enjoyed by everyone. They also have enormous intrinsic value, whereby they support clean coastal and marine environments and wildlife, and play an important role in keeping our climate stable. However, traditional activities (transport, fishing, tourism) now sit alongside, and often compete with, more recent activities such as mineral extraction and renewable energy production. The unsustainable use of our seas threatens the fragile balance of marine ecosystems.

The aim of the European Union’s Marine Strategy Framework Directive (MSFD), adopted in 2008, is to more effectively protect the European marine environment. The Directive aims to achieve Good Environmental Status (GES) of the EU’s marine waters by 2020, and each Member State is required to develop a strategy for this. As the Directive follows an adaptive management approach, these strategies must be kept up-to-date and reviewed every six years.


New tsunami alert system tested in Portugal:

New tsunami alert system tested in Portugal

Man climbing down a ladder on a pier
The experimental alert system being tested in Setubal consists of a digital panel and a sea level measurement device
© EU, 2014

A new tsunami alert system developed by the JRC was tested in Setubal, Portugal, today. The experiment confirmed the effectiveness of using a sea level measurement device to trigger automatic alerts. This new system could be used to detect any kind of tsunami before they reach the sea shore, and issue automatic warnings to populations at risk in order to facilitate timely evacuations.

The experimental alert system being tested in Setubal consists of a digital panel and a sea level measurement device. The digital panel, equipped with data receivers, a siren and loudspeakers, has been placed in the Albarquel Park, by the sea. The sea level measurement device is positioned 3 kilometres from the digital panel along Setubal’s coast. During the test conducted on 2 October 2014, a measurement device was placed inside a mechanical simulator, which simulates a rise in the sea level corresponding to a tsunami wave. When the measurement device detects a significant rise in the sea level, it transmits a signal to the digital panel, which then alerts people present in the park via the digital panel, the loudspeakers and the siren.

The experiment confirmed that the real time analysis and transmission of the signal from the measurement device to the alert panel is reliable. It also demonstrated that sea level measurement can be efficient as a triggering mechanism for a tsunami alert device. Increasing the distance between the measurement device and the sea shore would increase the lead time before the arrival of the wave and thus provide more time to evacuate.

The alert device can also be activated manually, if necessary, or in cases of tsunamis caused by earthquakes, the panel can be automatically activated using JRC software, which estimates the wave height and travel time on the basis of the epicentre and magnitude of the earthquake. Connecting the alert device with local sea level measurement systems will allow automatic activation of the alarm also in case of dangerous waves of non-seismic origin, created by undersea landslides or collapsing volcanoes. In such cases, existing alert systems based on seismic signals wouldn’t be able to send a prior warning. The decision to allow automatic or manual alerting is to be assumed by the local authorities in charge of people evacuation.

The experiment is part of a European research activity which studies new advanced methods to improve disaster alerting mechanisms and to shorten the transmission time of alerts. The JRC is conducting the experiment in close collaboration with the Portuguese Institute of Sea and Atmosphere (IPMA).



workshop “QUANTITATIVE CLADISTICS AND USE OF TNT – 2nd Edition”, June 29 – July 3, 2015.

Dear colleague,

Registration is open for the workshop “QUANTITATIVE CLADISTICS AND USE OF TNT – 2nd Edition”, June 29 – July 3, 2015. Instructors: Dr. Goloboff and Dr. Szumik (Conicet, Argentine).
PLACE:  Facilities of the Centre de Restauració i Interpretació Paleontologica, Els Hostalets de Pierola,  Barcelona (Spain).WEBPAGE: http://www.transmittingscience.org/courses/phylo/cladistics/

Intro and Basics. Parsimony and phylogenetic systematics. Character optimisation and mapping. Most parsimonious reconstructions and specific changes. Input/output in TNT. Dataset formats. Using GB->TNT to create matrices. Instruction files. Options for graphic output (SVG, metafiles). Creation of “batch” files. Editing trees. Handling tree files. Groups of trees, characters and taxa.

– Tree calculation. Tree searches. Exact solutions, Wagner trees, branch-swapping. Local and global optima. Use of multiple addition sequences. Improving search strategies. Factors which affect the efficiency of tree-searches. Constraints and “timeouts”.

Ambiguity and consensus; summarizing results. Zero-length branches and collapsing rules. Types of consensus and their use; improving consensus trees; supertrees. Pruned consensus. Comparison of tree-topologies; SPR distances.

Character weighting. Successive and implied weighting. Auto-weighted optimization. Refining character weighting with blocks; taking into account missing entries. User-defined weighting functions.

– Group supports. Concept of group support. Bremer supports; how to calculate them; search of suboptimal trees. Problems with Bremer supports; absolute and relative Bremer support. Partitioned Bremer support and individual Bremer supports. Measures based on resampling; effect of search strategies and collapsing rules. Problems with resampling methods.

– Tree search in large and difficult data sets. Special search algorithms. Sectorial searches. Ratchet and drifting. Tree fusing. Combining different algorithms. Driven searches and stabilization of consensus.

– Scripting. Automation of decisions to go beyond simple commands. Flow control. Decisions. Expressions, user variables, and internal variables. Design of simple scripts.

This course  is co-organized by Transmitting Science, the Institut Catalá de Paleontologia M. Crusafont and the Centre de Restauració i Interpretació Paleontologica. Places are limited and will be covered by strict registration order.

Please feel free to distribute this information between your colleagues if you consider it appropriate.

With best regards
Juan Vicente Bertó Mengual
Communication Manager
Transmitting Science

If you want to receive information about specific courses, please subscribe (http://www.transmittingscience.org/subscription.htm) selecting those topics of your interest.



Por un Medio Ambiente en Equilibrio

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