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.

BioSyst.EU, 15-18 augusti 2017

The third meeting of BioSyst.EU will be organised by the Swedish Systematics Association in corporation with the University of Gothenburg and will be held August 15–18, 2017 at the Wallenberg Conference Centre, Gothenburg, Sweden. The meeting will feature invited thematic symposia as well as open sessions on systematic and evolutionary biology.

More information on the meeting, and registration forms, are available at www.conferencemanager.se/BiosystEU2017.

BioSyst.EU represents European scientists dealing with topics of systematic biology. It considers itself as a collaborative counterpart to the Consortium of European Taxonomic Facilities (CETAF) where European Natural History Institutions have joined, whereas in BioSyst.EU individual scientists are to be represented via their national or regional societies. Svenska Systematikföreningen is a member of BioSyst.EU.

PhD position in Plant Systematics, University of Gothenburg

http://www.gu.se/english/about_the_university/announcements-in-the-job-application-portal/?languageId=0&disableRedirect=true&id=19144&Dnr=767692&Type=E

Project description
Species is one of the most fundamental units in biology. Despite this, there is a lot of controversy on how the species category is characterized. Evolutionary biology in particular and biology in general have recently gained enormously from conceptual and empirical developments in our understanding of how species are formed and related. However, much of this has been based on small amounts of information in models that may be statistically misleading. With the increased availability of DNA sequence data at the genomic level, it is time to develop statistical tools and models that make full use of this information. In this project, we will develop and refine statistical methods that are based on the multispecies coalescent to derive species delimitations and assignments. The recently developed methods that infer species trees while taking uncertainty in species delimitation into account offer an excellent baseline.
We will extend these to take morphological and geographical trait data into account, and merge them with species networks in this project, we will make heavy use of the large empirical data sets from projects studying reticulate phylogenetics among ca 750 species of Sileneae.
The student will become a member of the Scandinavian research school in biosystematics, ForBio (http://www.forbio.uio.no).

Job assignments
The main task is to conduct the PhD thesis work under supervision, which includes development of the PhD student’s methodology experience, analytical skills, and theoretical depth and breadth.
Techniques used within the project include preparation of DNA suitable for modern mass sequencing techniques, and bioinformatics handling and analysis of the data. The studies will be conducted mostly as laborative studies. Shorter periods may also be spent as field work. Specific research topics associated with the research project include plant systematics, bioinformatics, and phylogenetics.

Third cycle education
Admission to third cycle education is aiming at a PhD in Natural Science, specialising Biology. The education runs for four years of fulltime studies, containing three years of thesis work, and one year of academic education i.e. course work and literature studies. A selection of courses at the Department/Faculty is available, but national/international courses can also be selected. Some teaching and/or course administration can be included which extends the contract to the same extent.

Eligibility
The qualifications for education on a doctoral level are: degree in advanced level, at least 240 university points, of which 60 are on an advanced level, or in an other way acquired similar knowledge.

Assessment
Regulations for the evaluation of qualifications for education on a doctoral level are given in SFS 1998:80.

We are seeking a highly motivated person for PhD studies in evolutionary plant systematics with emphasis on species tree models
Good communication skills (written and spoken) in English are necessary.

Specialization within bioinformatics and experience of modern mass DNA sequencing protocols is advantageous.

Basic knowledge in computer programming is a merit.

The top ranked candidates will be selected for an interview, which might be held in English and could also be performed by phone /skype.

Additional information
The application must include:

A short cover letter with the applicant’s justification for the application, i.e., that describes how the applicant meets the selection criteria (max. one A4 page)

An attested list of qualifications (CV)

Examination certificates and a transcript of courses with grades

A copy of the Masters thesis (or equivalent)

Employments certificates and other documents deemed important by the applicant

Contact information for at least two referees that are familiar with the applicant’s qualifications

The application should be written in English.

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User manual for the portal

Related information

For further information please contact

Bengt Oxelman, Professor
+46(0)31 768 26 78
bengt.oxelman@gu.se

Henrik Aronsson, Head of Department
+46(0)31-786 48 02
henrik.aronsson@bioenv.gu.se

bioenv.gu.se

Labour union

SACO: Klas Eriksson
+46(0)31-7861989
klas.eriksson@gu.se

OFR/S: Anna Nilsson
+46(0)31-786 43 00
anna.nilsson@globalstudies.gu.se

SEKO: X X
+46(0)31-786 1173
seko@gu.se

Closing date

2016-06-30

Appointment Procedure

Please apply online.

Complementary documents, such as publications/books should be sent to the following address: University of Gothenburg, Department of Biology and Environmental Sciences, Att: Ingela Lyck, Box 463, 405 30 Gothenburg

Reference number should be clearly stated when sending complementary documents.

The University of Gothenburg promotes equal opportunities, equality and diversity.

Applications will be destroyed or returned (upon request) two years after the decision of employment has become final. Applications from the employed and from those who appeal the decision will not be returned.

Appointments Procedure for Teachers

Appointments Procedure for Teachers

Bengt Oxelman
Department of Biology and Environmental Sciences
Göteborg University
Box 461
SE-40530 Göteborg
Sweden
Tel. +46 31 786 2678

Faktura: Box 1023, 831 29 Östersund. Referens ”3130BOXEBE”

inbjudan till systematikdagarna

[for English, see below]

Uppsalas två universitet välkomnar alla till Systematikdagarna 2016, ett forum för vetenskapligt utbyte, spjutspetsforskning och överraskningar för alla intresserade av biologisk systematik. De kommer att gå av stapeln 21-22 november på evolutionsbiologiskt centrum. Vi utlovar många intressanta föredrag, workshops och postrar.

Priset blir som vanligt lågt, men det kompenseras av god mat och trevligt umgänge. Se till att redan nu anteckna dessa datum i din kalender.

Formell anmälning från augusti via web-formulär.

Är du intresserad av att bidraga med föredrag eller fråga om något, hör gärna av dig redan nu till följande adress:

systematikdagarna2016@ebc.uu.se

Under Systematikdagarna avhålls också Svenska Systematikföreningens årsmöte.

———————————————————————————————–

You are most welcome to Systematikdagarna 2016, the annual gathering for everyone with an interest in biological systematics, this year hosted by the Uppsala universities November 21-22. Please make sure to note these days in your calender.

Formal registration from August, via SSF webpage [you will be notified].

The price will be very low. Talks, workshops, poster session, good food and merriments are on the agenda.

If you like to contribute, e.g. with a talk, please tell us. You reach us at

systematikdagarna2016@ebc.uu.se

 

 

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