Getting Started with Nextflow

Objectives Understand

What a workflow management system is.

Understand the benefits of using a workflow management system.

Explain the benefits of using Nextflow as part of your bioinformatics workflow.

Explain the components of a Nextflow script.

Run a Nextflow script.

Introduction to Bioinformatics workflows with Nextflow and nf-core

Getting Started with Nextflow

Address of the bookmark: https://carpentries-incubator.github.io/workflows-nextflow/aio/index.html

http://www.interpretomics.co/

Address of the bookmark: https://github.com/sib-swiss/training-collection

Center for Integrative Genomics, University of Lausanne, Switzerland

Two postdoctoral positions (2 years with possible extensions up to 5 years) are available immediately in the evolutionary genomics group of Henrik Kaessmann.

We are seeking highly qualified and enthusiastic applicants with strong skills in computational biology/bioinformatics, preferably also with experience in data mining and comparative or evolutionary genome analysis.

We have been interested in a range of topics related to the functional evolution of genomes from primates (e.g., the emergence of new genes and their functions) and other mammals (e.g., the origin and evolution of mammalian sex chromosomes). In the framework of a recently launched series of projects, a large amount of transcriptome and genome (e.g., epigenome) data are being produced by the wet lab unit of the group using next generation sequencing technologies for a unique collection of tissues from representative mammals and outgroup species (e.g., birds). Topics of current projects based on these data include the origins and/or evolution of protein-coding genes, alternative splicing, microRNAs, long noncoding RNAs, and dosage compensation.

The postdoctoral fellow will perform integrated evolutionary/bioinformatics analyses based on data produced in the lab and available genomic data. The specific project will be developed together with the candidate.

The language of the institute is English, and its members form an international group that is rapidly expanding. The institute is located in Lausanne, a beautiful city at Lake Geneva.

For more information on the group and our institute more generally, please refer to our website: http://www.unil.ch/cig/page7858_en.html

Please submit a CV, statement of research interest, and names of three references to: Henrik Kaessmann (Henrik.Kaessmann@unil.ch).

Webpage : http://www.unil.ch/cig/page7858.html

More at https://www.nibmg.ac.in/uploads/3c5d4da3fb31bef490a218805408c858.pdf

We are looking for a highly motivated candidate with a PhD degree in
Bioinformatics or a related field. Candidates are expected to have a
strong background in evolutionary biology and/or comparative functional
genomics. Additional experiences in single cell functional genomics
analyses, statistics and computational data analyses are a plus, as is
an interest in comparative developmental (EvoDevo) questions.

We offer a dynamic and interactive research environment with state-of-the
art research facilities, good research funding and internationally
competitive salaries.

The Tschopp lab (www.evolution.unibas.ch/tschopp/research/)
studies the gene regulatory mechanisms of cell type
specification and evolution in vertebrates. See also our
preprints at https://doi.org/10.1101/2024.03.26.586769 and
https://doi.org/10.1101/2024.11.28.625862 Applications should include
a motivation letter, a CV, a list of publications, a statement about
research interests, as well as the names and contact details of at
least two referees. Applications (in the form of a single .pdf file)
should be sent to Patrick Tschopp (patrick.tschopp@unibas.ch); review
of applications will begin on January 1st 2025, and will continue until
the position is filled.

Find the detail paper at http://bib.oxfordjournals.org/content/early/2013/06/25/bib.bbt043.full

Address of the bookmark: http://bib.oxfordjournals.org/content/early/2013/06/25/bib.bbt043.full

Here’s a curated list of the top websites offering bioinformatics job opportunities and postdoctoral fellowships worldwide.

1. General Bioinformatics Job Portals

These platforms are ideal for bioinformaticians seeking jobs in diverse sectors:

• Nature Careers: A trusted resource for job seekers in the sciences, Nature Careers offers bioinformatics roles globally. Their specialized search function allows you to filter jobs by keyword, location, and more.

  • Explore Bioinformatics Jobs on Nature Careers

• Science Careers: A job board from the AAAS, this site focuses on STEM jobs, including numerous bioinformatics opportunities in academia and industry.

• Euraxess: Euraxess is the go-to platform for researchers looking for jobs, fellowships, and funding across Europe and beyond. It lists both bioinformatics roles and research grants.

  • Search Bioinformatics Jobs on Euraxess

• ResearchGate Jobs: ResearchGate is widely known as a platform for researchers to share publications, but it also has a robust job board featuring bioinformatics positions globally.

• FindAPostDoc: This site is dedicated to helping postdoctoral researchers find positions, with bioinformatics being a popular category.

• Academic Positions: Targeting academic roles worldwide, Academic Positions lists bioinformatics jobs at universities and research institutions.

• PostdocJobs.com: Specializing in postdoctoral roles, this platform is a great resource for early-career researchers looking for bioinformatics-related positions.

• Scholarship Positions: In addition to jobs, Scholarship Positions provides information on scholarships, fellowships, and grants related to bioinformatics.

2. Fellowship and Training Opportunities in Bioinformatics

For those seeking fellowships or specialized training, these organizations offer postdoctoral programs, grants, and research opportunities:

• NIH Office of Intramural Training and Education: The National Institutes of Health offer extensive research training programs for postdocs, including those in bioinformatics.

• NSF Research Opportunity Awards: The National Science Foundation funds bioinformatics research at predominantly undergraduate institutions, providing fellowships and grants.

• Top U.S. Universities: Many prestigious U.S. institutions, including Harvard, Berkeley, Yale, MIT, Johns Hopkins, UCSD, and Cornell, offer postdoctoral opportunities in bioinformatics.

3. Country-Specific Job and Fellowship Resources

If you're targeting a specific region, these platforms offer bioinformatics opportunities tailored to their respective countries:

Canada

• CAPS/ACPP: The Canadian Association of Postdoctoral Scholars provides a job board, including bioinformatics roles in academia.
• Banting Postdoctoral Fellowships: A prestigious fellowship program for postdocs in bioinformatics and related fields.
• Mitacs Elevate: A Canadian initiative offering fellowships to connect postdoctoral researchers with industry partners.

United Kingdom

• UKRI: The UK Research and Innovation body funds bioinformatics research and offers various grants.
• The Royal Society: Provides funding schemes for researchers in bioinformatics.
• Marie Skłodowska-Curie Actions: The MSCA funds fellowships and doctoral programs across Europe, including bioinformatics-related projects.
• Wellcome Trust: Offers research funding and career development opportunities in health-related fields, including bioinformatics.

Europe

• EMBO Fellowships: The European Molecular Biology Organization supports bioinformaticians through fellowships and career grants.
• Max Planck Society: A leading research organization offering bioinformatics positions and fellowships across Europe.
• Helmholtz Association: A major research organization in Germany offering bioinformatics roles in various disciplines.
• Leibniz Association: Offers research opportunities, including bioinformatics, across its numerous institutes.

Australia and New Zealand

• Australian Research Council: Offers funding and research schemes, including in bioinformatics.
• Top Universities: Universities like Sydney, Melbourne, and Queensland have research programs in bioinformatics.

Asia

• Japan Society for the Promotion of Science (JSPS): Offers fellowships for international researchers in bioinformatics.
• Top Institutions: Universities like NUS, CAS, and IISc are leading hubs for bioinformatics research.

Middle East

• Qatar Research, Development, and Innovation (QRDI): Offers research opportunities in bioinformatics.
• KAUST: A leading university in Saudi Arabia offering bioinformatics research positions.

Africa

• African Academy of Sciences: Provides career opportunities and research funding in bioinformatics across Africa.

Conclusion

The field of bioinformatics is full of exciting opportunities for those with the right skills. Whether you are looking for a postdoc position, research funding, or a long-term job in industry, these platforms are an excellent starting point. Explore, apply, and take the next step in your bioinformatics career!