BioAcoustica: an online repository and analysis platform for wildlife sound

•

1 recomendación•593 vistas

Edward Baker

What is BioAcoustica? Why did we develop it? Where is it going?

Ciencias

BioAcoustica: an online repository and
analysis platform for wildlife sound
Ed Baker
http://dx.doi.org/10.6084/m9.figshare.1591866

5
Problems with Physical Media
Bulky
Must be digitised before
doing modern analyses
Harder to search than
digital
Hard to annotate sections
of sound

7
Other Sound Archvies: Digital Archives
British Library Sound Archive
Tierstimmenarchiv, Berlin
● Many thousands of recordings. Can search
online then visit/request recordings
● Small number of recordings online

8
Other Sound Archvies: Digital Archives
Macaulay Library
● Thousands of recordings, available online
● Online analysis if you use the Raven browser
plugin

9
Other Sound Archvies: Digital Archives
xeno-canto
● Community project / citizen science
● 250,000+ plus recordings
● All available online

10
Other Digital Resources (Orthoptera)
Archive Orthoptera
recordings
Taxa Taxonomic
focus
Geographic focus
Macaulay 9282 262 Ensifera North America
DORSA-SYSTAX 9176 550 Orthoptera Europe (Ecuador, South East
Asia)
Tierstimmenarchiv 1093 66 Orthoptera
Acrididae
Europe
SINA n.a. (440) Ensifera North America
Orthoptera Species
File
n.a. 776 Orthoptera World-wide
GBIF 3973 XX XX World-wide
Reide, K (Article In Prep)

11
Other resources
Data behind many (most?) bioacoustics
publications are not published.
● Hard to re-use data
● Hard to validate studies

12
Why BioAcoustica?
Take features from other projects
● Community can upload
● Online analyses
Add new features
● Online annotation of recordings
Utilise existing infrastructure
● Scratchpads

13
Scratchpads
EU funded Virtual Research Environment (EDIT;
ViBRANT)
● Handles taxonomy, specimens, references,
media files, taxon descriptions
● Contributes data to GBIF; Encyclopedia of Life
● Integration with Taverna/BioVeL for analysis
using grid computing

16
Developments: Annotations
Annotation
● Describing what a recording contains
● Which part is the spoken introduction?
● Are there regions with excessive background
noise?
● What parts can I use for analysis?
● Deal with multiple species per recording

17
Developments: BioVeL
Biodiversity Virtual e-Laboratory
● Runs workflows on a grid computing
infrastructure
BioAcoustica
● Comes with a set of general acoustic analyses
combined into a BioVeL workflow

18
Developments: Analyse by default
Every time an annotation is made on a recording
indicating there is a clear call, that section of
audio is analysed

21
Future plans
(Some initial thoughts after a few discussions)

22
Future plans
Preserving collections:
Sharing/synchronising recordings and metadata
between projects.
LOCKSS (Lots of Copies Keeps Stuff Safe)

23
Future plans
Single interface for discovery (taxon neutral)
Global Biodiversity Informatics Facility?

24
Future plans
A BioAcoustics workbench
● Shared tool development, shared analyses
● Standard datasets for testing against
● Taverna/BioVeL?

25
Thanks
BioAcoustica Team
Ben Price; Vince Smith; Simon Rycroft; Jon Hill
Taverna
Francisco Quevedo
Klaus Riede
Gregor Hagedorn

Más contenido relacionado

Similar a BioAcoustica: an online repository and analysis platform for wildlife sound

Computer-aided Inventories of Bioacoustic Diversity: First Results and Future needs. Talk presented at IBAC 2007 (Pavia). The wishlist is still pending... Wishlist and perspectives  User-friendly interfaces  Federated multimedia databases (GBIF?)  Unique identifiers for sound files  Metadata standards  searchable sound annotations (incl carrier frequency)  ...... more sound files Wishlist and perspectives  User-friendly interfaces  Portable tools (cricket detector): basic sound processing feature extraction local database access  searchable sound annotations (incl carrier frequency)  Federated multimedia databases (GBIF?)  ...... more sound files

Ibac2007 riede

Klaus Riede

Background / Purpose: The 21st century started with an impressive number of international biodiversity initiatives, such as the International Year of Biodiversity (2010) and the recently launched United Nations Decade on Biodiversity ( http://www.cbd.int/2011-2020/ ). Main conclusion: Most nations are now members of the Convention on Biological Diversity and expressed a strong commitment for safeguarding Earth´s biodiversity through their National Biodiversity Action Plans and work programs supporting taxonomy, such as the Global Taxonomy Initiative. Internet projects such as the Global Biodiversity Information Facility provide unprecedented opportunities for taxonomists and Natural History Museums to make their efforts visible through the federation of separate museum databases: users can search for species, visualise localities on a map and recall pictures of museum specimens made available by “Virtual Museums”. However, availability of multimedia data is still limited, particularly for type specimens. Taking European museums as an example, I demonstrate the potential of successful virtual museum projects and analyse priorities and needs for further digitisation, which is a pre-requisite for repatriation of biodiversity data from tropical countries. Improved access to collections is also among the main tasks of the recently established CETAF secretariat in Brussels ( Consortium of European Taxonomic Facilities ). This new institution will function as a European voice for taxonomy and systematics, and hopefully helps to sustain orphaned EU activities from former projects supporting taxonomy, such as the European Distributed Institute of Taxonomy .

nternational Biodiversity Projects and Natural History Museums: Current stat...

Klaus Riede

World wide access to biodiversity literature - The Biodiversity Heritage Library

BHL-Europe

Biodiversity Heritiage Library: progress and process

Phil Cryer

Digital audiovisual content has become an important communication channel in Science. The TIB|AV-Portal for audiovisual scientific-technical information meets the requirements to preserve such content and to provide innovative services for search and retrieval. Quality checked audiovisual content from Open Source Geoinformatics communities is constantly being acquired for the portal as a part of TIB's mission to preserve relevant content in applied computer sciences for science, industry, and the general public.

GIS Day 2015: Geoinformatics, Open Source and Videos - a library perspective

Peter Löwe

Digital Preservation Best Practices: Lessons Learned From Across the Pond

Benoit Pauwels

Digital Presentation Best Practices: Lessons Learned From Across the Pond

ULB - Bibliothèques

The Open Cloud Computing Interface (OCCI) specification set defines a general protocol and API applicable to many different cloud resource management tasks. OCCI began as a remote management API for IaaS model based Services, allowing for the development of interoperable tools for common tasks including deployment, autonomic scaling and monitoring. It has since evolved into a general-purpose flexible RESTful API framework with a strong focus on integration, portability, interoperability and innovation while still remaining highly extensible. OCCI is suitable to serve many other models in addition to IaaS, including e.g. PaaS and SaaS. The current release (v1.1) of OCCI has achieved a high degree of adoption and implementation in production in a wide variety of languages, projects, software products and application areas. The OCCI working group is in the process of developing an update of the OCCI specifications as version 1.2 with improvements that result from nearly four years of successful field experience. This version will be backwards compatible with v1.1 and will include: - A new JSON rendering to accompany updates to the existing HTTP and text renderings. - Minor updates of current OCCI core infrastructure model and specification. - New extensions that will include PaaS support, notifications support and SLA support. ?In addition, the OCCI group is considering best methods for support of additional features, including monitoring, key management and security, interdomain networking and direct interface support for popular batch systems through the Distributed Resource Management Application API (DRMAA) standard.

OCCI - The Open Cloud Computing Interface – flexible, portable, interoperable...

Alan Sill

ViBRANT—Virtual Biodiversity Research and Access Network for Taxonomy

Vince Smith

About the Virtual Conference With the expansion of digital data collection and the increased expectations of data sharing, researchers are turning to their libraries or institutional repositories as a place to store and preserve that data. Many institutions have created such data management services and see the data curation role as a growing and important element of their service portfolio. While some of the experience in managing other types of digital resources is transferrable, the management of large-scale scientific data has many special requirements and challenges. From metadata collection and cataloging data sources, to identification, discovery, and preservation, best practices and standards are still in their infancy. This Virtual Conference will explore in greater depth than traditional webinars some of the practical lessons from those who have implemented data management and developed best practices, as well as provide some insight into the evolving issues the community faces. It will include discussions related to certification of trusted repositories, provenance and identification issues around data, data citation, preservation, and the work of several repository networks to advance distribution of scientific information.

April 23 NISO Virtual Conference: Dealing with the Data Deluge: Successful Te...

National Information Standards Organization (NISO)

The iPlant Tree of Life Project and Toolkit

Naim Matasci

Introduction to eMonocot (Dave Simpson)

eMonocot

GBIF-Norway status for the 6th European GBIF nodes meeting April 2014

Dag Endresen

On Monday 7 December 2020, the selected consortia for the ARCHIVER prototype phase have been announced during a Public Award Ceremony. The Kick-off marks the beginning of the Prototype implementation Phase, where the three selected to move forward will build prototypes of their solutions including all components, and basic functionality, interoperability, and security tests will be performed by IT specialists from the buyers’ group.

Prototype Phase Kick-off Event and Ceremony

Archiver

NHM Data Portal: first steps toward the Graph-of-Life

Edward Baker

NHM Data Portal: first steps toward the Graph-of-Life

Vince Smith

Digital library initiatives in Turkey: A brief overview

Yasar Tonta

Improvements of experimental technologies forces biologists to face a deluge of data that require relevant tools and sufficient resources to be analyzed. The cloud helps bioinformatics experts to define virtual appliances with pre-installed tools and workflows, and helps scientists to deploy them, on demand, on national research infrastructures. Presented by Christophe Blanchet and Clément Cauthey at the EGI Community Forum in Manchester, UK in April 2013.

Providing Bioinformatics Services on Cloud

stratuslab

Scripting Life: ViBRANT's Kickoff meeting

Vince Smith

Multilingual challenges and ongoing work to tackle them at Europeana

Antoine Isaac

Similar a BioAcoustica: an online repository and analysis platform for wildlife sound (20)

Ibac2007 riede

nternational Biodiversity Projects and Natural History Museums: Current stat...

World wide access to biodiversity literature - The Biodiversity Heritage Library

Biodiversity Heritiage Library: progress and process

GIS Day 2015: Geoinformatics, Open Source and Videos - a library perspective

Digital Preservation Best Practices: Lessons Learned From Across the Pond

Digital Presentation Best Practices: Lessons Learned From Across the Pond

OCCI - The Open Cloud Computing Interface – flexible, portable, interoperable...

ViBRANT—Virtual Biodiversity Research and Access Network for Taxonomy

April 23 NISO Virtual Conference: Dealing with the Data Deluge: Successful Te...

The iPlant Tree of Life Project and Toolkit

Introduction to eMonocot (Dave Simpson)

GBIF-Norway status for the 6th European GBIF nodes meeting April 2014

Prototype Phase Kick-off Event and Ceremony

NHM Data Portal: first steps toward the Graph-of-Life

Digital library initiatives in Turkey: A brief overview

Providing Bioinformatics Services on Cloud

Scripting Life: ViBRANT's Kickoff meeting

Multilingual challenges and ongoing work to tackle them at Europeana

Más de Edward Baker

Data Sharing in Ecoacoustics

Edward Baker

Ecoacoustic Challenges: UKAN Soundscapes Workshop

Edward Baker

Towards automated monitoring of Orthoptera (and some other noisy stuff)

Edward Baker

Phasmids as Pests of Agriculture and Forestry

Edward Baker

Phasmid Study Group: Name changes talk (Summer Meeting 2014)

Edward Baker

NHM MSc: Automated Acoustic Identification

Edward Baker

Measuring Impact: Towards a data citation metric

Edward Baker

New tools for monitoring biodiversity and environments

Edward Baker

Building highways in the informatics landscape

Edward Baker

Scratchpads & Citizen Science

Edward Baker

What will a digitial Natural History Museum look like in 10 years time?

Edward Baker

Biodiversity Informatics of the Cyperaceae: Where we stand and where we’re he...

Edward Baker

Biodiversity Informatics at the Natural History Museum

Edward Baker

The story of a Wikipedia page

Edward Baker

ViBRANT Citizen Science: Intro

Edward Baker

European initiatives

Edward Baker

Scratchpads Training Course

Edward Baker

Nature Live!: Cockroaches from the beginning (May 2012)

Edward Baker

Scratchpads Intro: Swiss Orchid Foundation

Edward Baker

Swiss Orchid Foundation Scratchpads and ViBRANT overview

Edward Baker

Más de Edward Baker (20)

Data Sharing in Ecoacoustics

Ecoacoustic Challenges: UKAN Soundscapes Workshop

Towards automated monitoring of Orthoptera (and some other noisy stuff)

Phasmids as Pests of Agriculture and Forestry

Phasmid Study Group: Name changes talk (Summer Meeting 2014)

NHM MSc: Automated Acoustic Identification

Measuring Impact: Towards a data citation metric

New tools for monitoring biodiversity and environments

Building highways in the informatics landscape

Scratchpads & Citizen Science

What will a digitial Natural History Museum look like in 10 years time?

Biodiversity Informatics of the Cyperaceae: Where we stand and where we’re he...

Biodiversity Informatics at the Natural History Museum

The story of a Wikipedia page

ViBRANT Citizen Science: Intro

European initiatives

Scratchpads Training Course

Nature Live!: Cockroaches from the beginning (May 2012)

Scratchpads Intro: Swiss Orchid Foundation

Swiss Orchid Foundation Scratchpads and ViBRANT overview

Último

Stages in the normal growth curve

Areesha Ahmad

Molecular markers are identifiable DNA sequences used to locate genes associated with specific traits or genetic conditions. A molecular marker is a specific gene fragment present at a specific position called ‘locus’ (pleural loci) in the genome of a cell. In the pool of unknown DNA or in a whole chromosome, these molecular markers help in identification of particular sequence of DNA at particular location.

Molecular markers- RFLP, RAPD, AFLP, SNP etc.

Silpa

PSYCHOSOCIAL NEEDS. in nursing II sem pptx

Suji236384

Digital Dentistry.Digital Dentistryvv.pptx

MohamedFarag457087

Human genetics..........................pptx

Silpa

Clean In Place(CIP).pptx .

Poonam Aher Patil

Introduction of DNA analysis in Forensic's .pptx

rohankumarsinghrore1

Ultrasound color Doppler imaging has been routinely used for the diagnosis of cardiovascular diseases, enabling real-time flow visualization through the Doppler effect. Yet, its inability to provide true flow velocity vectors due to its one-dimensional detection limits its efficacy. To overcome this limitation, various VFI schemes, including multi-angle beams, speckle tracking, and transverse oscillation, have been explored, with some already available commercially. However, many of these methods still rely on autocorrelation, which poses inherent issues such as underestimation, aliasing, and the need for large ensemble sizes. Conversely, speckle-tracking-based VFI enables lateral velocity estimation but suffers from significantly lower accuracy compared to axial velocity measurements. To address these challenges, we have presented a speckle-tracking-based VFI approach utilizing multi-angle ultrafast plane wave imaging. Our approach involves estimating axial velocity components projected onto individual steered plane waves, which are then combined to derive the velocity vector. Additionally, we've introduced a VFI visualization technique with high spatial and temporal resolutions capable of tracking flow particle trajectories. Simulation and flow phantom experiments demonstrate that the proposed VFI method outperforms both speckle-tracking-based VFI and autocorrelation VFI counterparts by at least a factor of three. Furthermore, in vivo measurements on carotid arteries using the Prodigy ultrasound scanner demonstrate the effectiveness of our approach compared to existing methods, providing a more robust imaging tool for hemodynamic studies. Learning objectives: - Understand fundamental limitations of color Doppler imaging. - Understand principles behind advanced vector flow imaging techniques. - Familiarize with the ultrasound speckle tracking technique and its implications in flow imaging. - Explore experiments conducted using multi-angle plane wave ultrafast imaging, specifically utilizing the pulse-sequence mode on a 128-channel ultrasound research platform.

(May 9, 2024) Enhanced Ultrafast Vector Flow Imaging (VFI) Using Multi-Angle ...

Scintica Instrumentation

Chemistry 5th semester paper 1st Notes.pdf

Sumit Kumar yadav

Factory Acceptance Test( FAT).pptx .

Poonam Aher Patil

GBSN - Microbiology (Unit 3)

Areesha Ahmad

www.seribangash.com The Mariana Trench is one of the most remarkable geological features on Earth. Here are some details about it: Location: The Mariana Trench is located in the western Pacific Ocean, east of the Mariana Islands. It stretches for about 2,550 kilometers (1,580 miles) and is known as the deepest part of the world's oceans. Depth: The trench reaches incredible depths, with its deepest point known as the Challenger Deep, which plunges down to approximately 10,984 meters (36,037 feet) below sea level. To put this into perspective, if Mount Everest, the tallest mountain on Earth, were placed at the bottom of the Challenger Deep, its peak would still be over 2 kilometers (1.25 miles) underwater. Formation: The Mariana Trench was formed by the subduction of the Pacific Plate beneath the Mariana Plate. This process creates a deep trench as the heavier Pacific Plate is forced beneath the lighter Mariana Plate. Geological Features: The trench is characterized by steep, V-shaped valleys, and its walls are composed of highly compressed sedimentary rock. At the bottom of the trench, there are also large amounts of marine sediment. Pressure: The pressure at the bottom of the Mariana Trench is immense, reaching over 1,000 times the pressure at the surface. This extreme pressure creates a challenging environment for exploration and makes it difficult for organisms to survive. Exploration: Despite its extreme conditions, the Mariana Trench has been the subject of numerous scientific expeditions and explorations. One of the most famous explorations was the dive to the Challenger Deep by Swiss scientist Jacques Piccard and U.S. Navy Lieutenant Don Walsh in 1960. More recently, in 2012, filmmaker James Cameron made a solo dive to the bottom of the Challenger Deep in the Deepsea Challenger submersible. Biological Discoveries: Despite the harsh conditions, the Mariana Trench is home to a surprising variety of life forms, including unique species of deep-sea fish, crustaceans, and microbial life. Some organisms have adapted to survive in the extreme pressure and darkness of the trench. Environmental Importance: Studying the Mariana Trench provides valuable insights into the geology, biology, and oceanography of the deep sea. It also helps scientists better understand the processes that shape the Earth's crust and the distribution of life in the oceans. Conservation: Due to its remote location and extreme depths, the Mariana Trench has remained relatively untouched by human activity. However, there is growing concern about the potential impacts of deep-sea mining and pollution on this fragile ecosystem, highlighting the need for conservation efforts to protect this unique environment. https://seribangash.com/barber-shop-business-complete-guide-for-beginners/ https://seribangash.com/legend-virat-kohli-in-cricket-history/

The Mariana Trench remarkable geological features on Earth.pptx

seri bangash

FAIRSpectra - Enabling the FAIRification of Spectroscopy and Spectrometry

Alex Henderson

CURRENT SCENARIO OF POULTRY PRODUCTION IN INDIA

Dr. TATHAGAT KHOBRAGADE

Zoology 5th semester notes( Sumit_yadav).pdf

Sumit Kumar yadav

Locating and isolating a gene, FISH, GISH, Chromosome walking and jumping, te...

Silpa

GBSN - Biochemistry (Unit 1)

Areesha Ahmad

development of diagnostic enzyme assay to detect leuser virus

NazaninKarimi6

Bhiwandi Bhiwandi ❤CALL GIRL 7870993772 ❤CALL GIRLS ESCORT SERVICE In Bhiwan...

Monika Rani

GBSN - Microbiology (Unit 2)

Areesha Ahmad

BioAcoustica: an online repository and analysis platform for wildlife sound

1. BioAcoustica: an online repository and analysis platform for wildlife sound Ed Baker http://dx.doi.org/10.6084/m9.figshare.1591866

2. Where are we, and where are we going?

3. 3 Other Sound Archives: Physical Media

4. 4 Other Sound Archives: Physical Media

5. 5 Problems with Physical Media Bulky Must be digitised before doing modern analyses Harder to search than digital Hard to annotate sections of sound

6. 6 Problems with Physical Media

7. 7 Other Sound Archvies: Digital Archives British Library Sound Archive Tierstimmenarchiv, Berlin ● Many thousands of recordings. Can search online then visit/request recordings ● Small number of recordings online

8. 8 Other Sound Archvies: Digital Archives Macaulay Library ● Thousands of recordings, available online ● Online analysis if you use the Raven browser plugin

9. 9 Other Sound Archvies: Digital Archives xeno-canto ● Community project / citizen science ● 250,000+ plus recordings ● All available online

10. 10 Other Digital Resources (Orthoptera) Archive Orthoptera recordings Taxa Taxonomic focus Geographic focus Macaulay 9282 262 Ensifera North America DORSA-SYSTAX 9176 550 Orthoptera Europe (Ecuador, South East Asia) Tierstimmenarchiv 1093 66 Orthoptera Acrididae Europe SINA n.a. (440) Ensifera North America Orthoptera Species File n.a. 776 Orthoptera World-wide GBIF 3973 XX XX World-wide Reide, K (Article In Prep)

11. 11 Other resources Data behind many (most?) bioacoustics publications are not published. ● Hard to re-use data ● Hard to validate studies

12. 12 Why BioAcoustica? Take features from other projects ● Community can upload ● Online analyses Add new features ● Online annotation of recordings Utilise existing infrastructure ● Scratchpads

13. 13 Scratchpads EU funded Virtual Research Environment (EDIT; ViBRANT) ● Handles taxonomy, specimens, references, media files, taxon descriptions ● Contributes data to GBIF; Encyclopedia of Life ● Integration with Taverna/BioVeL for analysis using grid computing

14. 14 Scratchpads

15. 15 Scratchpads

16. 16 Developments: Annotations Annotation ● Describing what a recording contains ● Which part is the spoken introduction? ● Are there regions with excessive background noise? ● What parts can I use for analysis? ● Deal with multiple species per recording

17. 17 Developments: BioVeL Biodiversity Virtual e-Laboratory ● Runs workflows on a grid computing infrastructure BioAcoustica ● Comes with a set of general acoustic analyses combined into a BioVeL workflow

18. 18 Developments: Analyse by default Every time an annotation is made on a recording indicating there is a clear call, that section of audio is analysed

19. 19 Developments: Link to Publications

20. 20 Making research data available

21. 21 Future plans (Some initial thoughts after a few discussions)

22. 22 Future plans Preserving collections: Sharing/synchronising recordings and metadata between projects. LOCKSS (Lots of Copies Keeps Stuff Safe)

23. 23 Future plans Single interface for discovery (taxon neutral) Global Biodiversity Informatics Facility?

24. 24 Future plans A BioAcoustics workbench ● Shared tool development, shared analyses ● Standard datasets for testing against ● Taverna/BioVeL?

25. 25 Thanks BioAcoustica Team Ben Price; Vince Smith; Simon Rycroft; Jon Hill Taverna Francisco Quevedo Klaus Riede Gregor Hagedorn

BioAcoustica: an online repository and analysis platform for wildlife sound

Recomendados

Recomendados

Más contenido relacionado

Similar a BioAcoustica: an online repository and analysis platform for wildlife sound

Similar a BioAcoustica: an online repository and analysis platform for wildlife sound (20)

Más de Edward Baker

Más de Edward Baker (20)

Último

Último (20)

BioAcoustica: an online repository and analysis platform for wildlife sound