Workshop on Inselect, NRM 24-25 October

Workshop on Inselect – A demonstration of a software which automates the cropping of individual images of specimens from whole-drawer scans preceded by a half-day mini symposium focusing on mass-digitization and computer vision.

24-25 October, 2016.
NRM, Stockholm, Sweden.
The workshop is hosted by the Department of Genetics and Bioinformatics at Naturhistoriska riksmuseet (Swedish Museum of Natural History, NRM) and SYNTHESYS. It will bring together leading international and local researchers, working on different aspects of digitization of natural history collections, image analyses and computer vision. First day will feature presentations by invited speakers followed by the one and a half day Workshop on Inselect, a computer tool that automates the cropping of individual images of specimens from whole-drawer scans and similar images that are generated by digitization of museum collections.
During the first half of the workshop we will learn some of the key Inselect features on provided sample images. For the second half, participants are encouraged to bring along some representative images together with any related information such as details of metadata that needs to be captured. Images should be in the format and at the full resolution at which they were taken. Some example images are TIFF files generated by a SatScan scanner at NHM, either images of drawers with pinned insects or of microscope slides arranged in a grid of between 400 and 800 MB. https://naturalhistorymuseum.github.io/inselect/pages/gallery.html
Everybody is welcome! The symposium will be free of charge, but registration is required. Coffee/tea will be served during breaks for the first 50 registered participants.
Please feel free to distribute this invitation to people/mailing-lists that you think might find this workshop interesting.

Miroslav Valan, NRM

Kurs: Phylogenetics, phylogenomics, citizen science and entrepreneurship (BIG 4 Fall Workshop 2016)

BIG 4 Fall Workshop 2016

Phylogenetics, Phylogenomics, Citizen science and Entrepreneurship

Dates: Mon Oct 10 – Tue Oct 18, 2016

Venue: Tovetorp research station (http://www.zoologi.su.se/tovetorp/)

Description

The BIG4 fall workshop 2016 has two main themes. One theme is focused on phylogenetics, phylogenomics and bioinformatics, and is intended to provide students with an introduction to these topics, focused on skills that will be useful in their PhD research projects. There will be a mixture of lectures and practicals; students are encouraged to bring their own datasets and analysis problems. The other theme is citizen science and entrepreneurship, and this part of the course will provide broad introductions, exercises, and inspiration for students interested in pursuing these subjects as part of their current or future activities.

The workshop is primarily aimed at BIG 4 students but (except for the Friday morning session) is open to outside participants as well. We have room for up to 10 additional outside participants on a first come first served basis. Outside participants may choose to come for only part of the course, if they wish.

Course registration and fee

Register for the course no later than September 28 using the form at this web site: http://bit.ly/2c6i6v0. Outside student participation will be confirmed on September 29. If you cancel past that date, we may very well have to charge you the course fee anyway.

There will be a fee for course, accommodation and food. We expect the total cost to be approximately 2,000 SEK/day for students participating for part of the course, and approximately 15,000 SEK in total for those students taking the entire workshop. Students will receive an invoice after the course is finished.

Schedule Overview

Monday October 10
Fredrik Ronquist. Introduction to statistical inference. Bayesian phylogenetic inference and Markov chain Monte Carlo simulation.
Fredrik Ronquist. Stochastic models of evolution. Introduction to MrBayes. Exercises using MrBayes.

Tuesday October 11
Fredrik Ronquist. Divergence time estimation: node dating and total-evidence dating. Statistical biogeography. Model testing, model averaging and other special topics.
Fredrik Ronquist. Phylogenetic graphical models. Introduction to RevBayes. Exercises using MrBayes and RevBayes.

Wednesday October 12
Erik Gobbo. De novo genome sequencing: next generation sequencing and genome assembly.
Chris Wheat. Gene finding, genome annotation and phylogenomic inference.
Chris Wheat, Erik Gobbo. Genome assembly, gene finding, genome annotation and phylogenomics exercises. Questions, discussion.

Thursday October 13
Rodrigo Esparza-Salas. Introduction to metabarcoding.
Daniel Marquina. Metabarcoding: special topics.
Rodrigo Esparza-Salas, Daniel Marquina. Metabarcoding exercises.

Friday October 14
BIG 4 Midterm Review [Only BIG 4 participants].
BIG 4 Midterm Review [Only BIG 4 participants].

Saturday October 15
Johan Nylander. Handling bioinformatics data in a unix environment. Bioinformatics exercises. Bring your own data and questions!

Sunday October 16
Free day for social activities. Food will be served as usual.

Monday October 17
Inga von Sydow. Why you should become an entrepreneur.
Inga von Sydow, Lyubomir Penev, Eduardo Pareja, Karin Carlsson. Round table discussion on entrepreneurship in biosystematics, informatics and genetics.
Karin Karlsson (Savantic AB). Training session: Steps in the entrepreneurship process.

Tuesday October 18
Karoly Makonyi. A personal view on citizen science.
Karin Carlsson. Gamification and viral effects: a case study.
Jakob Jönsson. Citizen science in cosmology.
Devin Sullivan. [Title TBA].
Erik Thorelli. Bionote – A citizen science platform for logging and sharing species sightings
Miroslav Valan. A brief history of citizen science and its potential in the era of big data.
Miroslav Valan, Karoly Makonyi. Roundtable discussion on citizen

Perl course: Perl Programming with Application to Bioinformatics Oct 10-14

A course in Perl Programming with Application to Bioinformatics (2 hp) will run from Oct 10-14 at SciLifeLab Uppsala. The deadline for application is Sep 5.

This course is highly recommended for anyone that wants to start using scripting in Perl for bioinformatics or any biological data analysis.

Full information and details of how to apply is available here:
https://www.scilifelab.se/events/perlht16/

Welcome!

Best regards,
Matthew Webster and Andreas Wallberg

The honeybee genomics research group
Dept of Medical Biochemistry and Microbiology
Uppsala University

Last chance to apply for two SIU and ForBio courses

SIU and ForBio course: Biodiversity data management and Open data

Nov 2-5, Tartu, Estonia

What are the modern, efficient, mistake-proof ways to collect and manage field and lab data, identifiers, traits, and environmental variables? How can you store your data to easily integrate with external databases?
This hands-on SIU and ForBio course on Biodiversity data management and Open data covers the basics of data collecting, data management, and publishing Open Data.

Last chance to apply, deadline 22 August!

http://www.forbio.uio.no/events/courses/2016/Open%20data

SIU and ForBio course: Polypores as tools in forest conservation

Sep 19-23, Lammi Biological Station, Finland

Polypores are dominant wood decomposers in boreal forests, and the basis of the saprobic wood web. Polypores are used as indicators of high conservation value forests in Nordic countries, and during this course one will learn how to identify polypores and selected corticioid fungi, focusing on indicator species. Also you will be familiarized with the concept of indicator species and indexes in practical use. The course includes lectures and daily field work in different types of forests, including old-growth forests.

Last chance to apply, deadline 22 August!

http://www.forbio.uio.no/events/courses/2016/Polypores

ForBio course: Phylogenomics – Extended deadline

The ForBio course: Phylogenomics has an extended application deadline: September 1st!

ForBio course: Phylogenomics
http://www.forbio.uio.no/events/courses/2016/phylogenomics.html

Time and place: Nov 14, 2016 – Nov 18, 2016, Natural History Museum, University of Oslo, Norway.
Teachers: Torsten Hugo Struck, NHM, UiO and Patrick Kück, NHM London.

Objectives: Advances in high-throughput sequencing and genomics have revolutionized research in evolutionary biology and systematics. The use of genomics data in phylogenetic analyses has brought new challenges in terms of data handling and analysis. This course aims to help those that have basic experience in bioinformatics and molecular phylogenetics, and have projects focused on high-throughput sequencing data and phylogenetics, to become acquainted with tools, programs and pipelines for phylogenomics and want to contact phylogenomic studies beyond the standard also addressing potentially confunding biases in their datasets.

Prerequisites: Basic knowledge of command line interaction, regular expressions, UNIX, sequence data and alignments, model-based phylogenetic analyses, model testing, Bayesian inference, is a prerequisite for participation. Pre-course exercises on command line, regex and UNIX will need to done, submitted and passed to ensure that all participants have an equal minimum level at start.

NB: This course consists of two parts, week I (14-18 Nov 2016) and week II (in March or April 2017). We will provide the exact dates as soon as possible. The first week covers the basic foundation of phylogenomic studies. Lectures and labs in week II will build upon this and focus on dissecting the phylogenetic signal in the dataset and detecting possible misleading biases such as long branches and compositional heteroegenities. Strategies for thorough sensitivity analyses in phylogenomic studies will be part of this week.

Maximum number of participants is 26.

Application deadline is September 1, 2016.

For more information and application go to the website: http://www.forbio.uio.no/events/courses/2016/phylogenomics.html

Contact Hugo de Boer (hugo.deboer@nhm.uio.no) or Torsten Hugo Struck (t.h.struck@nhm.uio.no) for more information.
All the best,

ForBio/Hugo

GU and ForBio course: Life and Earth History

The evolution of life on Earth is inevitably linked with the geological and climatic history that has dramatically changed available habitats and resources over time. In this course we will explore how geological and paleoclimatic evidence and paleontological and neontological data can be combined to better understand the interplay between Earth history and the evolution and biogeography of organisms. We will provide key concepts about biostratigraphy and fossil preservation and their crucial role in dating events in deep time. We will touch upon several major events of climate changes and landmass dynamics in different part of the world and at different geological times, such as the formation of the Himalayan mountain range, the Paleocene–Eocene Thermal Maximum (PETM; ~ 55 Ma), and the formation of a land bridge connecting the North and South American continents. A special focus will be given to the effects of these events on local and global biodiversity and its spatial distribution. Further, we will demonstrate computational methods that can help us investigating the dynamics of origination, dispersal, and extinction of organisms using fossil occurrence data. This course will also include practicals providing training in computational (paleo)biology to infer macroevolutionary dynamics and instill or reinforce skills in python and R computing.

Course content
The course includes: 1) formal lectures on earth history and its links to biodiversity dynamics; 2) workshops on the use of computational methods to infer macroevolutionary processes from fossil data with hands-on practicals; 3) visiting the “The history of life and its teeming diversity” exhibition at the Natural History Museum of Gothenburg.

Outcomes
After completion of the course the PhD student will have gained insights on important geological and climatic events that have characterized Earth history and inevitably impacted biodiversity and evolution. They will also have a better understanding of the paleontological and geological evidence that these events left and how they can be used to understand the origin and history of life on Earth, at different geographic and temporal scales. Finally, participants will learn how to setup and carry out macroevolutionary analyses using the software PyRate (https://github.com/dsilvestro/PyRate) to infer origination, extinction and preservation rates from fossil occurrence data.

Required reading
A list of scientific publications required for the course will be distributed among confirmed students two weeks before the start of the course.

Assessment
Preparation of a short research proposal (powerpoint presentation and two page executive summary) to be presented and submitted 10 days after course completion.

Course teachers
Christine D. Bacon, Carina Hoorn, Carlos Jaramillo, Daniele Silvestro

The University of Gothenburg course plan can be found here.

Application deadline is August 12th, 2016. Apply here. Plan to book travel arrangements that weekend.

A 1.5 ECTS course certificate will be given to students that pass the course, either by GU or ForBio depending on registration.

Contact the course leaders Daniele Silvestro or Christine D. Bacon, or ForBio leader Hugo de Boer for more information.

Research School in Biosystematics – ForBio: course overview

The Research School in Biosystematics – ForBio is organising a number of relevant courses in the summer and autumn this year, and we invite you to apply to these courses, or forward this overview to interested colleagues for further dissemination to students and postdocs.

Looking forward to seeing you at our courses! Hugo – ForBio

—————
Transmitting Science and ForBio course: Introduction to Electron Microscopy for Life Sciences
Time and place: Jul 5, 2016 09:00 AM – Jul 8, 2016 06:00 PM, Universitat Autònoma de Barcelona (UAB), Barcelona (Spain).
http://www.forbio.uio.no/events/courses/2016/electronmicroscopy.html

SIU and ForBio course: Dead Wood Course
Time and place: Aug 8, 2016 – Aug 11, 2016, Lammi Biological Station, Finland
http://www.forbio.uio.no/events/courses/2016/Deadwood

ForBio and STIRs course: DNA barcoding – from theory to applications
Time and place: Aug 22, 2016 – Aug 26, 2016, Zoology building, Medicinaregatan 18, Gothenburg
http://www.forbio.uio.no/events/courses/2016/barcoding.html

ForBio course: Marine Annelids in the Norwegian Sea
Time and place: Sep 4, 2016 – Sep 10, 2016, NTNU, Sletvik Field Station , Norway
http://www.forbio.uio.no/events/courses/2016/Annelid%20field%20course

SIU and ForBio course: Polypores as tools in forest conservation
Time and place: Sep 19, 2016 – Sep 23, 2016, Lammi Biological Station, Finland
http://www.forbio.uio.no/events/courses/2016/Polypores

ForBio and UiO: Mycology field course
Time and place: Sep 26, 2016 – Sep 30, 2016, Biological Station Drøbak, Norway
http://www.forbio.uio.no/events/courses/2016/mycology.html

ForBio course: Introduction to Bioinformatics for Biosystematics
Time and place: Oct 3, 2016 – Oct 7, 2016, Biological Station Drøbak, Norway
http://www.forbio.uio.no/events/courses/2016/bioinfointro_2016.html

DEST and ForBio course: Philosophy of Biological Systematics
Time and place: Oct 10, 2016 – Oct 14, 2016, Biological Station Drøbak
http://www.forbio.uio.no/events/courses/2016/philbiolsyst.html

DEST and ForBio course: Basics of Taxonomy – describing, illustrating and communicating biodiversity
Time and place: Oct 10, 2016 09:00 AM – Oct 21, 2016 06:00 PM, Zoology house, Medicinaregatan 18, Gothenburg, Sweden
http://www.forbio.uio.no/events/courses/2016/Basics%20of%20Taxonomy.html

ForBio course: Species Concepts and Species Delimitation
Time and place: Oct 24, 2016 – Oct 28, 2016, NTNU, Trondheim, Norway
http://www.forbio.uio.no/events/courses/2016/Species%20delimitation

SIU and ForBio course: Biodiversity data management and open data
Time and place: Oct 31, 2016 – Nov 4, 2016, Tartu, Estonia
http://www.forbio.uio.no/events/courses/2016/Open%20data

ForBio course: Phylogenomics
Time and place: Nov 14, 2016 09:00 AM – Nov 18, 2016 05:00 PM, Natural History Museum, University of Oslo
http://www.forbio.uio.no/events/courses/2016/phylogenomics.html

ForBio course: Species Concepts and Species Delimitation

The Research School in Biosystematics – ForBio invites you to:

ForBio course: Species Concepts and Species Delimitation
http://www.forbio.uio.no/events/courses/2016/Species%20delimitation

Time and place: Oct 24, 2016 – Oct 28, 2016, NTNU, Trondheim, Norway
Teachers: Kevin de Queiroz, Smithsonian Institution, Washington; Joan Pons, Mediterranean Institute for Advanced Studies (IMEDEA), Balearic Islands, Paschalia Kapli, Heidelberg Institute for Theoretical Studies

Course content
What is a species? Are they real entities we can define and diagnose? In this course you will learn about philosophical, conceptual, theoretical and practical issues around species concepts and the implication of their different definitions in ecological and conservation studies. Species boundaries in many organism groups are still in a state of flux, and for empirical species delimitation, finding appropriate character sets and analytical tools are among the greatest challenges. We will review the advantages and disadvantages of different types of data for species assessment and you will be introduced to the different methods for species delimitation based on DNA sequence data and interpretation of results. Students will gain hands-on-experience about distance and tree based methods for species delimitation, including the use of software such as CROP, ABGD, UCLUST, PTP, GMYC and BPP. We will generate stimulating discussion about the interpretation of results and the advantages and limitations of these methods.

Learning targets
• Understanding the implications of the different species concepts
• Pros and cons of different types of data for species assessments
• Gain an overview of different methods for species delimitation using DNA sequence data, and their advantages and limitations.
• Hands-on experience with distance and tree based approaches.

Credits: 3 ECTS
Level: PhD students, postdocs and researchers – with experience in phylogenetic analyses.
Participants: Maximum number of participants is 18.
Registration: http://www.forbio.uio.no/events/courses/2016/Species%20delimitation
Application deadline: October 1, 2016

ForBio/Hugo and Maria

ForBIO/STIRS Course: DNA barcoding from theory to applications

What? A course in DNA barcoding technique for species/OTU:s identification.

When? August 22-26, 2016

Were? Zoology building, Medicinaregatan 18, Gothenburg

Who arranges: STIRS and ForBIO in cooperation.

Learning targets:

• Understanding of the barcoding concept (including metabarcoding)

• Knowledge of e-DNA methods

• Knowledge of applications for barcoding

• Basic understanding of advanced techniques in lab and analysis

Read more here.