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Nederbragt, Lex
(2023).
Cognitive Load: what is it and how can we take it in consideration when teaching?
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Nederbragt, Lex
(2022).
Carpentry@UiO: Workshops for basic skills in programming and datamanagement at The University of Oslo (UiO).
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Nederbragt, Lex; Lemma, Roza Berhanu; Belova, Tatiana; Cheneby, Jeanne; Ibrahim, Mohamed & Akdeniz, Byram Cevdet
[Show all 7 contributors for this article]
(2022).
Oslo Bioinformatics Workshop Week 2022.
Show summary
December 7th-13th 2022 will see the very first Oslo Bioinformatics Workshop Week at the University of Oslo, Norway. This event is organised by the Student Committee of the Centre for Bioinformatics at UiO, in collaboration with the ISCB Regional Student group in Norway.
These workshops are open to the scientific community in Oslo and the surrounding area.
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Eliassen, June Edvarda; Bøe, Maria Vetleseter; Nederbragt, Lex & Gregers, Tone Fredsvik
(2021).
Motivasjon for beregningsorientert biologi og sammenhengen med matematikk R2 fra videregående opplæring.
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Nederbragt, Lex
(2021).
Using Jupyter for teaching programming to bachelor students in Bioscience.
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Fyhn, Marianne; Malthe-Sørenssen, Anders; Mørken, Knut Martin; Nederbragt, Alexander Johan; Odden, Tor Ole & Sundnes, Joakim
(2019).
Beregningsorientering og utdanningsutvikling.
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Nederbragt, Alexander Johan
(2019).
Learning from the Carpentries.
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Nederbragt, Alexander Johan
(2018).
Programmering og modellering i biovitenskapsutdanning.
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Reinar, William Brynildsen; Tørresen, Ole K.; Matschiner, Michael; Jentoft, Sissel; Nederbragt, Alexander Johan & Jakobsen, Kjetill Sigurd
(2018).
The impact of repetitive DNA on speciation rates in teleost fish.
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Tennøe, Simen; Mobarhan, Milad; Dragly, Svenn-Arne; Solbrå, Andreas Våvang & Nederbragt, Alexander Johan
(2017).
Teaching modelling to first-year biology students.
Show summary
The field of biology relies heavily on computations. This is not well reflected in education and the current undergraduate curriculum has little computational content. This results in a discontinuity between the education received by the students and the problems they face after graduation. The end result is that the students are not equipped to meet the requirements of modern research nor the tasks awaiting them in the industry. To remedy this problem, a new course, BIOS 1100 - Introduction to Modelling in Biology, will be held for the first time at the University of Oslo in fall 2017.
Currently, no available book combines biology and programming at an introductory level in a satisfactory way. Most textbooks teach both topics separately or expect the reader to know either biology or programming from before. We have therefore written our own textbook to be used as curriculum in this course. This book aims to teach programming and modelling to first year biology students through examples from biology. The book is based on a philosophy of just-in-time teaching where the programming concepts are introduced just when they are needed to solve the problem in hand. This puts the programming content in an unusual order in comparison to the traditional computer science curriculum while keeping the biology students motivated by the problems they solve. The examples are mainly from the three branches of biology: population dynamics, bioinformatics and evolution.
The purpose is to give biology students a practical understanding of programming and mathematical models. This will enable the understanding of mathematical models and encourage critical thinking. Programming allows much more realistic and inspiring problems to be addressed, enabling students to work on current research topics early on. The textbook is written using DocOnce (created by Hans Petter Langtangen), which enables us to compile the book to both LaTeX/PDF, HTML and Jupyter Notebooks.
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Nederbragt, Alexander Johan
(2017).
How I got infected by fish genomics - and how you can too.
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Nederbragt, Alexander Johan
(2017).
Teaching Researchers Basic Skills for Computational Research: the Software Carpentry Model.
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Sandve, Simen Rød; Hvidsten, Torgeir Rhoden; Lien, Sigbjørn; Rori, Rohlfs; Jakobsen, Kjetill Sigurd & Nome, Torfinn
[Show all 9 contributors for this article]
(2017).
Evolution after whole genome duplication - insights from the salmonids.
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Nederbragt, Alexander Johan
(2016).
In between lines of code - a blog about biology, sequencing, bioinformatics and more.
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Nederbragt, Alexander Johan
(2016).
SMRTwishes for SMRTsoftware for SMRTreads - a user’s perspective.
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Nederbragt, Alexander Johan
(2016).
The new Atlantic cod reference genome.
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Nederbragt, Alexander Johan & Lagesen, Karin
(2016).
The Carpentry effort at the University of Oslo.
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Eide, Marta; Puntervoll, Pål; Lille-Langøy, Roger; Goldstone, Jared V.; Tørresen, Ole Kristian & Nederbragt, Alexander Johan
[Show all 11 contributors for this article]
(2016).
Chemical warfare in the marine environment: genomic survey of the Atlantic cod (Gadus morhua) defensome reveals the absence of an important xenosensor.
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Nederbragt, Alexander Johan
(2015).
In between lines of code - a blog about biology, sequencing, bioinformatics and more.
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Star, Bastiaan; Jentoft, Sissel; Matschiner, Michael; Nederbragt, Alexander Johan; Kjesbu, Olav Sigurd & Berg, Paul Ragnar
[Show all 12 contributors for this article]
(2015).
Does historic DNA provide genomic evidence for recent selection in Atlantic cod?
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Nederbragt, Alexander Johan
(2015).
Bioinformatics breakout : Recent experiences from Oslo.
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Nederbragt, Alexander Johan
(2015).
Active learning strategies for bioinformatics teaching.
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Nederbragt, Alexander Johan
(2015).
A New, High Quality Reference Genome Assembly For Atlantic Cod.
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Nederbragt, Alexander Johan
(2015).
Local, central or cloud Why we chose to build our e-infrastructure for sequence analysis embedded in the university of Oslo HPC cluster.
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Brynildsen, William; Tørresen, Ole Kristian; Jakobsen, Kjetill Sigurd & Nederbragt, Alexander Johan
(2014).
Genomic sequence repeats in fish genomes.
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Tørresen, Ole Kristian; Jentoft, Sissel; Star, Bastiaan; Sandve, Geir Kjetil F.; Skage, Morten & Hansen, Marianne Helén Selander
[Show all 9 contributors for this article]
(2014).
A new, high quality reference genome assembly for Atlantic cod.
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Tørresen, Ole Kristian; Walenz, Brian; Grove, Harald; Lien, Sigbjørn; Knight, James & Star, Bastiaan
[Show all 15 contributors for this article]
(2014).
A new, high quality reference genome assembly for Atlantic cod.
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Matschiner, Michael; Star, Bastiaan; Berg, Paul Ragnar; Tørresen, Ole Kristian; Nederbragt, Alexander Johan & Hansen, Marianne Helén Selander
[Show all 11 contributors for this article]
(2014).
Population differentiation and local adaptation in Atlantic cod.
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Nederbragt, Alexander Johan
(2014).
The why and how of long reads for de novo genome assembly.
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Nederbragt, Alexander Johan
(2014).
Mix and match: using multiple sequencing technologies and assemblers for the new Atlantic cod genome.
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Nederbragt, Alexander Johan
(2014).
The why and how of long reads for de novo genome assembly.
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Nederbragt, Alexander Johan
(2013).
Repeat after me: Is our research reproducible (enough)?
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Nederbragt, Alexander Johan
(2013).
Using PacBio Reads to Improve and Validate the Assembly of the Complex Atlantic Cod Genome.
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Nederbragt, Alexander Johan
(2013).
The IPython Notebook: an introduction, and hands-on/live demo.
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Nederbragt, Alexander Johan
(2013).
Lessons learned from assembling the Atlantic cod genome.
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Nederbragt, Alexander Johan
(2013).
High Throughput Sequencing technologies.
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Nederbragt, Alexander Johan
(2013).
The IPython Notebook: an introduction, and hands-on/live demo.
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Loman, N.; Hadfield, James & Nederbragt, Alexander Johan
(2013).
Seqbench: Open-source benchmarking of sequence platforms and software.
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Nederbragt, Alexander Johan
(2013).
High Throughput Sequencing technologies at the Norwegian Sequencing Centre with a focus on genome assembly.
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Tørresen, Ole Kristian; Nederbragt, Alexander Johan; Miller, Jason Rafe; Walenz, Brian; Jentoft, Sissel & Jakobsen, Kjetill Sigurd
(2013).
Improving the Atlantic cod genome using long-read PacBio in combination with 454 and Illumina sequencing data.
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Tørresen, Ole Kristian; Nederbragt, Alexander Johan; Lagesen, Karin; Khelik, Ksenia; Rognes, Torbjørn & Jentoft, Sissel
[Show all 7 contributors for this article]
(2012).
Improving the cod genome with the use of multi-platform sequencing data.
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Nederbragt, Alexander Johan
(2012).
The bioinformatics of sequencing and assembling genomes - with a focus on the Atlantic cod and salmon genome projects.
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Nederbragt, Alexander Johan
(2012).
Experiences with Combining PacBio with Short Read Technology for Improved de novo Assembly of Complex Genomes.
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Nederbragt, Alexander Johan
(2012).
Experiences with Combining PacBio with Short Read Technology for Improved de novo Assembly of Complex Genomes.
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Nederbragt, Alexander Johan
(2012).
High-throughput sequencing og behovet for tungregneressurser.
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Nederbragt, Alexander Johan
(2012).
The best of both worlds - Combining PacBio with short read technology for improved de novo genome assembly.
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Nederbragt, Alexander Johan
(2012).
New High Throughput Sequencing technologies at the Norwegian Sequencing Centre - and beyond.
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Nederbragt, Alexander Johan; Tørresen, Ole Kristian; Skage, Morten; Tooming-Klunderud, Ave ; Hansen, Marianne Helén Selander & Jentoft, Sissel
[Show all 9 contributors for this article]
(2012).
The long jump: Long distance mate pairs and long PacBio reads for the Salmon Genome Project.
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Nederbragt, Alexander Johan
(2012).
New High Throughput Sequencing technologies at the Norwegian Sequencing Centre - and beyond.
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Nederbragt, Alexander Johan
(2012).
How and why I use blogging and twitter for science.
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Nederbragt, Alexander Johan; Tørresen, Ole Kristian; Khelik, Ksenia; Lagesen, Karin; Rounge, Trine Ballestad & Star, Bastiaan
[Show all 13 contributors for this article]
(2012).
Challenges and Opportunities for Improving the Atlantic Cod Genome Assembly and Annotation.
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Star, Bastiaan; Nederbragt, Alexander Johan; Jentoft, Sissel; Grimholt, Unni; Malmstrøm, Martin & Gregers, Tone Fredsvik
[Show all 18 contributors for this article]
(2011).
The genome of Atlantic cod reveals a unique immune system.
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Nederbragt, Alexander Johan; Lagesen, Karin & Malmstrøm, Martin
(2011).
Bioinformatic analysis of genomic data.
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Nederbragt, Alexander Johan
(2011).
How to sequence a large eukaryotic genome and how we sequenced the cod genom.
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Rounge, Trine Ballestad & Nederbragt, Alexander Johan
(2011).
The Atlantic Cod Genome Project.
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Nederbragt, Alexander Johan
(2011).
Next generation sequencing: research opportunities and bioinformatic challenges.