Författararkiv: Johan Nylander

Workshop on Inselect, NRM 24-25 October

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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)

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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

Summer school – ”Taming the BEAST”

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(Forwarded e-mail fro Chi Chang)

We are happy to announce our Summer School ”Taming the BEAST” and would kindly ask you to forward this email to interested students and PostDocs. We apologize if you receive this email more than once.

Phylogenetics and phylodynamics are central topics in modern biology. Phylogenetic inferences reconstruct the evolutionary relationships between organisms, whereas phylodynamic inferences reveal the dynamics that lead to the observed relationships. These two fields have many practical applications in disciplines such as epidemiology, developmental biology, paleontology, ecology and even linguistics. However, phylogenetics and phylodynamics are complex and fast-evolving fields. As such, inference tools are not easily accessible to researchers who are not from a computational background.

Taming the BEAST is a summer school focusing on the BEAST2 software and consisting of a mix of invited talks, lectures and hands-on tutorials by leading and renowned experts in the field (including several of the core developers of BEAST2). The aim of this summer school is to equip participants with the skills necessary to confidently perform their own phylogenetic and phylodynamic inferences in Bayesian settings, while providing them with a firm grasp of the theory behind those inferences. Participants are also highly encouraged to bring their own datasets along and to engage with the organizers and speakers to address any problems specific to their own datasets/analyses.

Registration is now open! We welcome applications from graduate students and early-career scientists in the life sciences. Preference will be given to applicants who are not from a computational background and applicants who have already collected/assembled a dataset that they need to analyze.

Invited speakers:

Tanja Stadler (ETH Zurich)
Alexei Drummond (University of Auckland)
Tracy Heath (Iowa State University)
Tim Vaughan (University of Auckland)
Oliver Pybus (University of Oxford)

Dates: June 26th to July 1st  (Registration deadline: March 15th)

Place: Engelberg, Switzerland

For more information regarding the program, registration, venue, etc, please visit the summer school website: https://www.bsse.ethz.ch/cevo/taming-the-beast.html

We hope to see you there,

the Taming the BEAST organizing team

Molecular-Clock Dating Using MrBayes – Seminar and Workshop

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Molecular-Clock Dating Using MrBayes – Seminar and Workshop

  • 22 April – Stockholm: 09:30-11:30, Rum 540, Botaniska Institutionen, Stockholms universitet
  • 23 April – Uppsala: 13:15-15:15, Lärosal 4, Evolutionsbiologiskt Centrum, Uppsala universitet

Chi Zhang*, Swedish Museum of Natural History, Stockholm
Johan Nylander, BILS/Swedish Museum of Natural History, Stockholm

MrBayes – the most often used software for Bayesian phylogenetic analysis – has included many new features since version 3.2. In this seminar, we will highlight some newly implemented functionality, with focus on the molecular-clock dating capacities of the current version (v.3.2.4). The seminar will consist of two parts, where following a presentation* giving the necessary backrground information, there will be a hands-on tutorial where participants are encouraged to bring their own data (and computers).

Abstract
There are two approaches on dating using molecular data: node dating and total-evidence dating. Node dating calibrates the internal nodes of the tree by assigning distributions using information from external sources, such as the fossil record. Total-evidence dating uses the morphological data from fossil record and morphological and sequence data from recent organisms together to infer the dates. Several steps involve in Bayesian dating analysis, including data partitioning, node or fossil age calibration, and setting priors for the tree and the molecular clock model. I will describe the available calibration probability distributions, clock tree priors – especially the fossilized birth-death prior for total-evidence dating, and relaxed clock models, through a step-by-step tutorial of MrBayes.

The program (MrBayes v.3.2.4) is available from http://mrbayes.net (alternatively https://sourceforge.net/projects/mrbayes/files/mrbayes)

Participants in the practical part are encouraged to bring their own computers with the software installed from the above mentioned URL’s.

Stockholm Phylogenomics Group – Talk at NRM 24 March: SUPERSMART. Change in time!

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Dear All!

Reminder and change of starting time!

Stockholm Phylogenomics Group announces – Upcoming talk at the Naturhistoriska riksmuseet, Stockholm, March 24.

Speakers: Alexandre Antonelli (University of Gothenburg),
Hannes Hettling and Rutger Vos (Naturalis Biodiversity Center,
the Netherlands)

Title: SUPERSMART: Ecology and evolution in the era of big data

Time: March 24 at 15:30-16:30

Venue: Room 525, Naturhistoriska riksmuseet, Stockholm

Host: Fredrik Ronquist

Abstract: Rapidly growing biological data volumes – including
molecular sequences and fossil records – hold an unprecedented
potential to reveal how evolutionary processes generate and
maintain biodiversity. However, most studies integrating these
data use an idiosyncratic step-by-step approach for the
reconstruction of time-calibrated phylogenies. We will present a
novel conceptual framework, termed SUPERSMART (Self-Updating
Platform for Estimating Rates of Speciation and Migration, Ages,
and Relationships of Taxa), and present our proof of concept for
dealing with the moving targets of biodiversity research. This
framework reconstructs dated phylogenies based on the assembly
of molecular and genomic datasets. The data handled for each step
are continuously updated as databases accumulate new records. We
believe that this emerging framework will provide an invaluable
tool for a wide range of hypothesis-driven research questions in
systematics and evolution. For more information please see

http://www.supersmart-project.org.

Stockholm Phylogenomics Group – Talk at NRM 24 March: SUPERSMART

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Stockholm Phylogenomics Group announces – Upcoming talk at the Naturhistoriska riksmuseet, Stockholm, March 24.

Speakers: Alexandre Antonelli (University of Gothenburg),
Hannes Hettling and Rutger Vos (Naturalis Biodiversity Center,
the Netherlands)

Title: SUPERSMART: Ecology and evolution in the era of big data

Time: March 24 at 15:00-16:00

Venue: Room 525, Naturhistoriska riksmuseet, Stockholm

Host: Fredrik Ronquist

Abstract: Rapidly growing biological data volumes – including
molecular sequences and fossil records – hold an unprecedented
potential to reveal how evolutionary processes generate and
maintain biodiversity. However, most studies integrating these
data use an idiosyncratic step-by-step approach for the
reconstruction of time-calibrated phylogenies. We will present a
novel conceptual framework, termed SUPERSMART (Self-Updating
Platform for Estimating Rates of Speciation and Migration, Ages,
and Relationships of Taxa), and present our proof of concept for
dealing with the moving targets of biodiversity research. This
framework reconstructs dated phylogenies based on the assembly
of molecular and genomic datasets. The data handled for each step
are continuously updated as databases accumulate new records. We
believe that this emerging framework will provide an invaluable
tool for a wide range of hypothesis-driven research questions in
systematics and evolution. For more information please see
http://www.supersmart-project.org.

Kurs i fylogenomik i Lund 5-9 Maj

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Kurs i fylogenomik, 5-9 Maj (2014), i Lund. Anmälan senast 21:a Mars. Inriktar sig till studenter med ”ingen eller begränsad erfarenhet i ämnet”. Lärare: Michel Cummings, Univ. Maryland. Se hemsidan: http://www.geneco.se/Courses/Spring-2014/Phylogenomics-5-9-May-2014

Phylogenomics course in Lund, May 5-9 (2014). Registration deadline: 21 March. Target audience: students having ”no or little prior experience in the field”. Teacher: Michael Cummings, Univ. Maryland. See web page: http://www.geneco.se/Courses/Spring-2014/Phylogenomics-5-9-May-2014

Seminar in the SPG seminar series: Alexandre Bouchard

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Nytt föredrag hos Stockholm Phylogenomics Group (www.phylogenomics.se), Fredag 19/4 kl 14-15 @ Science for Life Laboratory i Solna.

”Dear all,

I am happy to present Alexandre Bouchard in the SPG seminar series.

Place: Floor 2 lunchroom of Science for Life Laboratory

Date: Friday, April 19

Time: 14:00

Title: Phylogenetic Sequential Monte Carlo

Abstract: Bayesian phylogenetic methods rely on accurate approximations of intractable expectations over the space of phylogenies, a problem that has been traditionally approached almost exclusively using Markov chain Monte Carlo samplers. However, the advent of large scale phylogenetic problems and new high resolution models calls for complementary approaches. In this talk, I will describe one such complementary approach based on Sequential Monte Carlo methods. I will demonstrate the flexibility that can be achieved using extensions of standard particle filters, and show different applications we are currently working on. I will also describe a new method that we have developed to parallelize SMC algorithms, entangled Monte Carlo. This technique, based on the particle genealogy, can be applied to parallelize SMC calculations while keeping communication costs between nodes low.

/Lars Arvestad”

 

Stockholm Phylogenomics Group – Aktiviteter Hösten 2012

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Höstens aktiviteter för Stockholm Phylogenomics Group  är nu uppdaterade!

Se även www.phylogenomics.se.

 

 

Dear members of the Stockholm Phylogenomics Group (SPG):

This is the program for the first part of the fall semester; we are still working on the activities for the early winter. More information will be available on the SPG mailing list shortly before each event.

To add or delete names to the SPG list, contact me at fredrik.ronquist@nrm.se.

Cordially welcome to our activities!

For the SPG,

/Fredrik

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Stockholm Phylogenomics Group

Fall 2012 (Part 1)

Wednesday September 26, 15.15 Seminar

Room 306 (The Cramér Room) House 6, Kräftriket

Sebastian Höhna (Stockholm University): ”Estimating non-constant species diversification rates and patterns under incomplete, systematic species sampling”

Wednesday October 3, 13.00 Seminar

Small lecture hall (Lilla hörsalen), Naturhistoriska riksmuseet

Prof. Bernhard Misof (Zoologisches Forschungsmuseum Alexander König, University of Bonn): ”Phylogenomics and the evolution of insects – The 1KITE project”

Tuesday October 9, 15.00 Seminar and Software Demonstration

MIN-LIG seminar room (beyond mineral exhibit), Naturhistoriska riksmuseet

Prof. Bruce Rannala (University of California, Davis): ”Species delimitation using multilocus sequence data”

At 16.00, after the seminar, Bruce will demonstrate his and Ziheng Yang’s software for Bayesian species delimitation using multilocus sequence data.

Tuesday November 6, 15.00 Journal Club

Room 526, Naturhistoriska riksmuseet

We discuss Bouchard-Côté et al.: Phylogenetic Inference via Sequential Monte Carlo Syst Biol (2012) 61(4): 579-593

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