Conference PISCeS - 18-20 June 2023 at Guelph

for more info

Online Metabarcoding Course - March 6 to 31, 2023

It is time again for my online Metabarcoding course:

This course provides an overview of the state of current technology and the various sequencing platforms used. It consists of a series of online lectures and research exercises and will go over 4 weeks but is designed in a fashion that you can go through course content at your own pace and according to your own schedule with work worth 4-8h per week. The course is fully asynchronous to accommodate for participants from various time zones. We still strive to make it as interactive as possible.

I have updated course content to include the newest HTS technology and methods such as metagenomics and transcriptomics. 

Throughout the course, we will explore:

• High throughput sequencing
• Metabarcoding/Metagenomics
• Metabarcoding analytics
• Recent applications

The course consists of a series of online lectures, research exercises, and group discussions where you have a chance to review the state of current technology, the various platforms used and the suite of bioinformatics tools available for sequence analysis and data interpretation.

For more information please go on the course enrolment page at the University of Guelph.

Post-Doctoral Fellowship in Bioinformatics and Ecological Genomics, University of Guelph, Canada

I am looking for a new Postdoctoral Fellow. Here the official posting:

Land Acknowledgement
The University of Guelph resides on the treaty lands and territory of the Mississaugas of the Credit. We recognize this gathering place where we work and learn is home to many past, present, and future First Nations, Inuit, and Métis peoples. Our acknowledgement of the land is our declaration of our collective responsibility to this place and its peoples’ histories, rights, and presence.
 
General Information (Six PDF Positions Available)
This post-doctoral position will be part of the Food from Thought initiative funded through a Canada First Research Excellence Award: https://foodfromthought.ca/. Contributing to this large endeavour to improve food security and sustainability, our goal is to generate bioinformatics strategies for the prediction of biodiversity and ecosystem services from diverse data types, such as -omics data, digital photographs, and/or environmental data. Data analysis has begun to catch up with the pace of data generation, and in these times where understanding and mitigating the effects of climate change and feeding a growing human population is of utmost importance, we need to turn our sights on connecting different sources of data and extracting actionable meaning from them. The successful applicants will utilize existing and new biological and environmental datasets, along with additional external data, with the goal of predicting ecosystem services, ecosystem health status, and biodiversity metrics using approaches such as statistical learning, machine learning, and network analysis. This may include such important factors as pollination, invasive species resistance, pest control, trophic interactions, water quality, and others. Successful applicants will be part of a cohort of six postdoctoral scholars focused on bioinformatics and ecosystem services, who will work together with a multidisciplinary team of Principal Investigators, students, staff, industry members, and communities.
 
What We Offer
·       The opportunity to engage in creative and impactful research relevant for sustainability and 

        food security
·       The opportunity to collaborate with researchers in a variety of fields, including computer 

        science, statistics, ecology, evolutionary biology, and genomics
·       Guidance to build valuable skills and to be well prepared for diverse future careers (skills 

        include scientific research; collaboration; communication with diverse stakeholders; 

        technical skills relating to coding, data analysis, graphics, code review, and publishing of 

        bioinformatics tools)
·       Access to unique data sets and participation in collaborative partnerships with academics, 

        industry, and governmental agencies
·       Regular, inclusive, and supportive mentorship from multiple PIs with diverse expertise to 

        support your research, career, and impact/outreach goals
·       Participation in a collaborative working group of PDFs, workshops, and conferences
·       Some monetary support for professional development, workshop participation, and 

        conference attendance as well as open-access publishing
 
Specific Information (PDF in Bioinformatics and Ecological Genomics)
We are seeking candidates interested in developing bioinformatics tools for taxonomic and functional annotation of multi-kingdom samples. Data are generated from amplicon-based approaches and/or metagenomics/totalRNA. We want to estimate and potentially forecast how local biodiversity is shaped by regional diversity, functional shifts within communities, spatial gradients of biotic and abiotic factors, seasonal climatic constraints, local habitat heterogeneity, and anthropogenic stressors. 
Anticipated deliverables from the research include: one or more scientific publication(s), well-commented and documented code that is made publicly available by the end of the project such that that it is user friendly and can respond to future data availability. The successful PDFs will also be expected to participate in a PDF Working Group (which may include collegial discussion, collaboration, and/or reciprocal code reviews prior to publication), in annual Knowledge Mobilization Working Group Meetings, as well as in at least one relevant scientific conference. The successful applicant will also play a role in co-mentoring undergraduate or graduate students.
The selected candidate will be based in the research group of Dr. Dirk Steinke (Adjunct Professor of Integrative Biology & Bioinformatics) and will also benefit from working closely with a co-advisor with complementary expertise in statistics or computer science as well as other collaborators.
 
Required Qualifications & Attributes
·       Must hold a PhD in bioinformatics, evolutionary biology, molecular ecology, genomics, or a          

        related discipline
·       Published at least one first-authored paper in a peer-reviewed journal 
·       Experience with coding in at least one computer language (intermediate to advanced level 

        required; skills must include: data formatting and filtering, data exploration and quality 

        checking, graphics, data analysis; prior experience in usage of high-performance 

        computing resources an asset; prior experience in software development and code testing 

        an asset)
·       Experience with at least two of the following: statistical analysis, analysis of DNA 

        sequencing data, genome assembly, machine learning, and/or statistical learning, 
·       Commitment to transparent and reproducible science (evidence of this commitment could 

        include prior publication of code and/or a thorough methods section in your prior 

        publication(s))
·       Commitment to respectful interactions with others and to equity, diversity & inclusion 

        (evidence of this attribute could include: prior or planned mentorship activities or 

        collaborations; participation in relevant committees or working groups; your personal 

        communication practices, etc.)
 
 
Application Requirements
A completed application will consist of:
·       Cover letter describing your interest in the position and also highlighting how you meet the 

        required qualifications and attributes
·       Curriculum vitae (including education history, experience and skills, publications, 

        conference presentations, outreach or leadership activities, interests)
·       Names and contact information for three referees (You may feel to include academic 

        advisors, collaborators, and/or an individual you have mentored.)
·       PDF reprint of 1-3 publications (should be first author of at least one work published or in 

        press; pre-prints are welcome among the selected submissions)

Please combine all of the above components into a single PDF and email to:
Dr. Dirk Steinke: dsteinke@uoguelph.ca
 
Length of Appointment & Salary
The PDF position is available for two years. Goal setting will be completed collaboratively early in the position, and progression will be discussed through regular meetings and reviewed at the one-year mark. The salary is $47,000 Canadian dollars annually, plus 17.2% value in benefits. The selected candidate will also benefit through access to $5,000 in travel funds for workshops and conferences and at least $3,000 to publish in open-access venues.
 
Deadline
Review of applications will commence on December 15 and proceed until the position is filled. The start date will be as soon as possible thereafter (subject to discussion with the successful applicant).
 
Equity, Diversity & Inclusion
The Steinke lab strongly supports diversity in science, and applicants from under-represented racial, cultural, gender-identity, physical ability, and/or neurological spectrums are particularly encouraged to apply. Applications can be received immediately; however, evaluation of the applications will not commence until December 15, 2022 in order to allow for a diverse applicant pool to be evaluated.

Research support program La Tribuna in Colombia.

Great video about the research support program La Tribuna in Colombia.

An exemplary participatory science exercise: This video shows how the inhabitants of this region become 'biomonitors', people from the local community who, by sharing their expertise, generate a dialogue of traditional knowledge with students from different universities in Colombia. In turn, they learn about modern research methods.

The video is in Spanish but that's no problem. It is not a problem to understand the message.

Job announcement - NINA, Norway: Bioinformatician with focus on eDNA and DNA-metabarcoding

 NINA is among Norway’s largest applied ecology research institutes with approximately 300 employees. NINA´s staff conducts natural and social science research related to interactions between humans and nature. The company’s head office is located in Trondheim, adjacent to the Norwegian University for Science and Technology (NTNU) Gløshaugen campus. NINA also has satellite offices in Oslo, Lillehammer, Bergen and Tromsø, and a salmonid research station at Ims in Rogaland County. The position will be based in NINA´s Department for Aquatic Biodiversity in Trondheim.

NINA conducts high quality, applied research that is directly relevant to real world applications. Our projects are financed by a broad variety of private and public sector clients, including environmental managers, industry, and national and international research councils. NINA is a leading research institute in ecological genetics both nationally and internationally, hosting well-equipped modern lab facilities at our Trondheim location. We increasingly use genetic methods for mapping and monitoring of biodiversity on landscape to population levels, and for the detection and monitoring of invasive species, and threatened species. NINA runs several national monitoring projects involving eDNA from water, soil, and scat samples, analyzing diversity of fungi, plants, insects, fish, mammals and more. NINA therefore sees a strategic need for bioinformatic expertise in the genetic group in Trondheim, and wishes to expand the group with a permanent, full-time research technician in bioinformatics. 

Key tasks in the position will be bioinformatic processing of sequence data and database management, particularly in relation to environmental DNA applications. However, other types of biological data collected in NINA are also relevant for the position. Depending on their skills and preferences, the successful candidate may also be involved in writing of scientific reports and papers, statistical analyses, and graphic presentations of results.

The successful candidate will be independent and an initiative taker, preferably holding an MSc degree or equivalent in bioinformatics or biology, and with practical qualifications and experience with bioinformatic analyses, R, Bash, Python and SQL/database management. Experience with eDNA and DNA-metabarcoding data is an advantage. Competence within population genetics is a plus, but not a requirement for the position. You are proactive, a good communicator, and like to work in interdisciplinary teams. You like scripting and programming using large datasets and you can handle working with several projects at the same time. You are prepared for challenging and variable work and are flexible to meet the variation of tasks included in applied research.

The position will be based at the Department of Aquatic biodiversity in Trondheim, but the successful candidate is expected to work on a broad array of projects across all departments in NINA.

NINA has an international working environment, with employees from more than 25 nationalities. The working language in NINA is Norwegian and it is expected that the successful candidate for this position will learn Norwegian after starting in NINA, if the candidate is not already familiar with a Scandinavian language.

NINA offers

• Permanent position in one of Europe’s strongest environmental research institutes
• Payment according to scientific merits and experiences
• Flexible working hours
• Obligatory, attractive group pension scheme and insurance
• Attractive work environment in modern offices of high standard

Applications may be submitted on e-mail to siri.svendsen@nina.no. It must include a CV with information on education, relevant work experience, references, and, if relevant, list of scientific publications.

Competitive candidates will be invited for interview.

NINA works actively to create a more diverse and inclusive work environment, as well as to recruit more women into research positions. Researchers with a minority background, women, and candidates who contribute to a wider diversity are therefore encouraged to apply.

Enquiries about the positions can be made to:

Senior Scientist Frode Fossøy (frode.fossoy@nina.no, tel: +47 99692303)

Research Director Ingeborg Palm Helland (ingeborg.helland@nina.no, tel: +47 97654820)

Application deadline is 15 of September 2022.

PhD position on pond turtles and metabarcoding

The LOEWE Center for Translational Biodiversity Genomics (LOEWE-TBG) aims at making the genomic basis of biological diversity accessible for basic and applied research. Building on genome sequencing and analysis, LOEWE-TBG research topics range from comparative genomics, natural products genomics, and genomic biomonitoring to functional environmental genomics. LOEWE-TBG is based in Frankfurt am Main, Germany, and is a joint venture of the Senckenberg Gesellschaft für Naturforschung (SGN), Goethe-University Frankfurt, Justus-Liebig-University Giessen and Fraunhofer Institute for Molecular Biology and Applied Ecology.

Subject to funding approval LOEWE-TBG and the Senckenberg Gesellschaft für Naturforschung invite applications for a

PhD Position (m/f/d; 65%) in the EU-project

EMYS-R: A socio-ecological evaluation of wetlands restoration and reintroduction programs in favor of the emblematic European pond turtle and associated biodiversity: a pan-European approach

Project background: Over the last 3 decades, the EU has funded numerous projects for wetland restoration in favor of the European pond turtle. Yet the results of these measures need to be more intensely promoted. A key question remains unanswered: what are the most effective wetland restoration methods suitable for sustainable maintenance and recovery of the European pond turtle and associated wildlife throughout Europe?

EMYS-R consolidates an existing international network of researchers and stakeholders to share complementary knowledge on past, present and future wetlands, biodiversity and their management. It is a 3-year participatory action-oriented research project based on seminal theories in humanities, social and natural sciences. It aims at testing the hypothesis that higher degrees of wetland restoration can compensate for limited capabilities of captive bred turtles to settle in the wild, and assess how specifically such conservation actions benefit society by bringing together people and nature.

Your tasks:

The successful PhD candidate will be involved in the ecological assessment of wetland restoration, turtle reintroduction and consequences on local biodiversity including non-target species. While based in Frankfurt am Main, Germany, the candidate will spend a substantial amount of time at the German and French field sites, and will also be traveling to trainings and meetings in Poland and Latvia, contributors of the EMYS-R consortium. More specifically, the successful candidate will conduct the following tasks:

• Data collection: behavioral (animal-borne data loggers including GPS and time-depth-acceleration recorders), biometric/demographic (capture-mark-recapture protocols) and ecological (water, sediment, turtle-centered prey-predators feces samples) on the German study site in Neuburg am Rhein

• eDNA Metabarcoding of environmental (water and sediment) and ecological (turtle prey-predator feces) samples

• bioinformatic analyses of metabarcoding sequences for genomic biodiversity monitoring and food web analyses

• Data analyses of existing and formerly collected time series on turtle behavior, biometry and demography

• Support and then lead field sessions in Neuburg am Rhein

• Support with public perception seminars and workshops in Neuburg am Rhein

• Literature review on German-written grey literature about wetland renaturations and turtle reintroductions

• Writing scientific publications, contributing to national and international conferences, as well as to internal

  reports and international guidelines

 

Your profile:

• Master degree in Biology, Ecology, Environmental Sciences, or equivalent

• Programming experience with manipulating large database (Metabarcoding sequences, behavioral long time

  series)

• knowledge in R, MatLab and Linux desirable

• Experience in the molecular genetic lab

• Experience with Metabarcoding desirable

• Mastering multivariate statistics

• Interest in interdisciplinary approaches

• Proven capabilities in implementing field protocols in remote places in autonomy and within a team

• Able to team up within a large international consortium

• Professional communication skills within the scientific consortium, but also with local stakeholders

• Fluent (speech and writing/reading) in German and English

• Ideally you are owner of the driving license B, are easy with wetlands and are able to swim

  Salary and benefits are according to a full-time public service position in Germany (TV-H E 13, 65%). The contract should start as soon as possible – but no later than April 1st, 2022 - and will initially be limited for 3 years.

  The Senckenberg Research Institutes support equal opportunity of men and women and therefore strongly invites women to apply. Equally qualified handicapped applicants will be given preference. The place of employment is in Frankfurt am Main, Germany.

  Please send your application, mentioning the reference of this job offer (ref. #12-21008) before 14.01.2022 by e-mail (attachment in a single pdf document) and including a cover letter detailing research interests and experience, a detailed CV and a copy of your certification to:

  Senckenberg Gesellschaft für Naturforschung Senckenberganlage 25
  60325 Frankfurt am Main

  E-Mail: recruiting@senckenberg.de
  For more information contact Dr. Kathrin Theissinger (kathrin.theissinger@senckenberg.de).

Course: Introduction to DNA Barcoding

 Instructor - yours truly.

Early bird deadline - register soon!

The use of DNA Barcoding continues to enhance species identification and biodiversity conservation. Stay up-to-date with the latest research and join the growing industry with Introduction to DNA Barcoding. Take advantage of the opportunity to learn from prominent DNA researcher Dirk Steinke as he guides you through a variety of topics that showcase the different applications of DNA Barcoding. Course dates: January 17 to March 13, 2022 Don't forget to register by December 18, 2021 and save on tuition with our early bird pricing! Sign me up!