Welcome

 

The Biodiversity Service & Application Tracker is a collection of links to software, tools and resources useful to taxonomists. All applications and services are categorised into an expandable and potentially hierarchical system covering major biodiversity topics. The site was developed and initially populated with the help of the EDIT WP5. EDIT also certifies software to be compatible with EDIT's Platform for Cybertaxonomy, a variety of tools known to work together to assist taxonomic work.

In the long term after the project has finished (2011) we hope the site will be maintained by the user community.

Anonymous users can search for tools and suggest new software to be reviewed. They also have the option to file bug tickets and suggest new features for the system. If they register and create an account, they can write comments to any review or even write reviews themselves that then have to be released for publication by the EDIT site administrator.

Each review page is dedicated to a single version of an application or service. It provides details such as system requirements, interfaces and standards, information on licensing and cost and most important a review from editors as well as a comments section at the bottom that is open for everyone.

Call for Individual Research Grant Applications 2014

Date: 
Sunday, December 1, 2013 - 12:00 - Friday, January 31, 2014 - 12:00
Event Description and Information: 

News from IFS (International Foundation for Sciences)

PRE-ANNOUNCEMENT of Call for Individual Research Grant Applications 2014

 Call will open:           December 1, 2013

Call will close:           January 31, 2014

 

Anticipated announcement of results:  July 31, 2014.

 

Full details and instructions on the submission procedure will be made available here when the call opens.

The following information is also available now:

»  Eligibility criteria (including eligible countries)

»  Application Forms  (for both 1st and renewal Grants)

»  Guidelines in English

»  Directives en franҫais (Guidelines in French)

»  IFS Individual Research Approach

»  Research Areas funded by IFS

Building workflows with Taverna workbench

Date: 
Thursday, December 5, 2013 - 11:31 - Friday, December 6, 2013 - 11:31
Location: 

Manchester, UK

Event Description and Information: 

5-6 December 2013, School of Computer Science, Kilburn Building, The University of Manchester, UK. M13 9PL.

Time
Thu 5th Dec, 2013, 10:00 – 17:00
Fri 6th Dec, 2013, 09:30 – 16:00

Format
The course is a two-day hands-on training event. The course will accommodate 10-15 researchers. The program consists of introductory lectures, practical computer work, and discussions. Researchers will be contacted upon admission in order to consider their own research objectives for the course.

Target community & qualifications
The target community is developers and data scientists working in all areas of biodiversity research, for example taxonomy, ecology, environmental sciences, genetics, population genetics, species distribution and population modelling, bioinformatics, phylogenetics, or the like.

A pre-requisite for the course will be some level of exposure to computer programming, for example developing in R.

Objective
The training event will introduce participants to the BioVeL project, and teach the attendees how to:

  1. run workflows via the BioVeL portal
  2. develop workflows using the Taverna workbench,
  3. register and discover services in the biodiversity catalogue and 
  4. share workflows via myExperiment.

Background

In the last two decades the relationship between biodiversity and ecosystem function has become a central issue in ecology, while biodiversity loss has been identified as a major driver of ecosystem change. As a result, ecological research transforms into a species-rich scientific discipline with increased focus on the ability to document, study, and predict the biodiversity composition in ecosystems. However, the analysis of patterns of biodiversity over large temporal and spatial scales is still very difficult to achieve as it requires biologists and environmental scientists to integrate their expertise, data, and methodologies across the traditional biological disciplines.

The Biodiversity Virtual e-Laboratory, BioVeL, addresses this challenge. In the BioVeL, scientists and computer engineers are working together to develop tools for pipelining data and analysis into efficient analytical pipelines, called workflows. Workflows are complex digital data manipulations and modelling tasks that execute sequences of web services. BioVeL designs and deploys such workflows for a selected number of important areas in systematic, ecological, and conservation research, e.g. for the analysis of data sets with ecological, taxonomic, phylogenetic, and environmental information.

The workflows allow the researcher to

(i) explore, access, refine, and format large data sets from major data providers,
(ii) combine disparate data sets with the researchers' individual data, and
(iii) run complex and computationally intense analytical cycles.

Workshop topics
Introduction to the BioVeL technical infrastructure, practical workflow building using worked examples, utilising workflow components, discovering and registering services, sharing workflows.

Outcomes
After completion of course the participants are expected to be able to
-    Have an understating of the BioVeL infrastructure (Taverna workbench, portal, workflows, services)
-    Construct simple workflows in order to support their own biodiversity research
-    Discover and share workflows and webservices

Required preparation
-    Participants need to bring their own laptops.
-    Installation of the Taverna Workbench is required prior to the workshop. Simple online instructions will be provided.
-    Short CV/biography (½ page).
-    15 line research objectives, incl. any data you want to analyse and the scientific question you wish to address.

Program

Day 1

  • Session 1. will set the stage with a presentation of a scientific showcase based on a BioVeL Workflow, including a live demonstration of the workflow in action. We will continue with an overview of the BioVeL (www.biovel.eu) project, including a brief introduction to newly released workflows, including taxonomic data refinement, ecological niche modeling, metagenomic traits based analysis.
  • Session 2. will introduce the BioVeL technical infrastructure, including the Taverna Workbench, BioVeL Portal, myExperiment and Biodiversity Catalogue.
  • Session 3. will include a practical example of building a biodiversity workflow using the Taverna workbench. Including the discovery of services via biodiversity catalogue and sharing workflows via myExperiment.

Day 2

  • Session 3 continued.
  • Session 4. will include an introduction to building modular workflows using workflow components and a hands- on session where attendees will be able to address their own scientific questions by chaining together services discovered via biodiversity catalogue.

 

Registration Form

Introduction to workflows for taxonomic refinement, biogeographic analysis, and species distribution modelling

Date: 
Tuesday, November 26, 2013 - 11:27 - Wednesday, November 27, 2013 - 11:27
Location: 

Cardiff University, UK

Event Description and Information: 

26-27 November 2013, Cardiff University, UK

Background
In the last two decades the relationship between biodiversity and ecosystem function has become a central issue in ecology, while biodiversity loss has been identified as a major driver of ecosystem change. As a result, ecological research transforms into a species-rich scientific discipline with increased focus on the ability to document, study, and predict the biodiversity composition in ecosystems. However, the analysis of patterns of biodiversity over large temporal and spatial scales is still very difficult to achieve as it requires biologists and environmental scientists to integrate their expertise, data, and methodologies across the traditional biological disciplines.

The Biodiversity Virtual e-Laboratory, BioVeL, addresses this challenge by having scientists and computer engineers working together to develop tools for pipelining data and analysis into efficient analytical pipelines, called "workflows." Workflows are complex digital data manipulations and modeling tasks that execute sequences of web services. BioVeL designs and deploys such workflows for a selected number of important areas in systematic, ecological, and conservation research, e.g. for the analysis of data sets with ecological, taxonomic, phylogenetic, and environmental information.

BioVeL data refinement and ecological niche modelling workflows allow researchers to:

(i) explore, access, refine, and format large data sets from major data providers;

(ii) combine disparate data sets with the researchers' own data; and

(iii) run complex and computationally intense analytical cycles.

(iv) generate comparative maps of species distribution

Workshop Objective
The training workshop will teach the attendees in using the informatic tools and services developed by the BioVeL project to address research topics such as historical analyses, invasive species distribution modelling, endangered species distribution modelling, and dynamic modelling of ecologically related species. In particular, there will be  introductions to the BioVeL e-infrastructure, Taxonomic data cleaning, Taxonomic name resolution and synonym expansion, Ecological niche modelling, model testing, statistical analysis of GIS data, invasive and endangered species distribution modelling, historical comparison biodiversity from museum collections.

Outcomes
After completion of course the participants are expected to be able to
-    Perform their research using BioVeL e-infrastructure (portal, workflows, services)
-    Carry out research projects requiring including taxonomic data discovery and integration, and niche modelling
-    Initiate and participate in cross-disciplinary projects in biodiversity research

Required preparation
-    Participants need to bring their own laptops. All workflows offered will be browser-based and don’t need any desktop installations. A sample data set will be provided with each workflow.
-    Scientists should bring their own data and/or should have identified accessible data sources.

Target community & qualifications
This workshop is designed for scientists with a solid background in any of the relevant areas in biodiversity research, e.g. taxonomy, ecology, environmental sciences, genetics, population genetics, species distribution and population modelling, bioinformatics, phylogenetics, etc. It is desirable that the attendees are working or planning to work with taxonomic revisions, biodiversity inventories, ecological assessments, descriptive studies, conservation projects, or analyses for the management of natural protected areas.

Format
The course is a two-day hands-on training event. 10-15 researchers will be admitted. The program consists of introductory lectures, practical computer work, and discussions.

After a short individual presentation, Day 1 will be dedicated to the preparation of data using BioVeL Data Refinement Workflow. The morning will focus on a general demonstration of the tool and exercise with a provided data set. In the afternoon, participants will work with their own data set and/or data from public sources. 

In Day 2 we will demonstrate the Ecological Niche modelling workflows, ask participants to practice with a provided data set. Then participants will run the workflows with their data prepared during day 1, addressing the scientific issues of their research interests.

To participate in the workshop, an application is required, and includes the following information:

  • Short CV/biography
  • 10 line explaning your scientific project objectives
  • Short description of the data you want to analyse, indication their origin (personal collection and/or public repositories)

Registration is available here.
Application deadline: 18 October, 2013
Notice of Admittance: 25 October, 2013

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