Previous courses at NBIS
Introduction to Data Management Practices
2024-04-23 to 2024-04-25 (3 days)
Deadline 2024-03-22
Solna
More info
This course will introduce important aspects of Research Data Management through a series of lectures and hands-on computer exercises. The course is intended for researchers that want to take the first steps towards a more systematic and reproducible approach to analysing and managing research data. **Application instructions** National course open for PhD students, postdocs, researchers and other employees within all Swedish universities. The course is geared towards life scientists wanting to take the first steps towards a more systematic and reproducible approach to analysing and managing research data. **Fee** We charge a fee for onsite course occasions, to be paid by invoice to NBIS. This includes lunches, coffee and snacks. _Please note that NBIS **cannot** invoice individuals._Introduction to Biostatistics and Machine Learning
2024-04-22 to 2024-04-26 (5 days)
Deadline 2024-03-24
Uppsala
More info
National course open for PhD students, postdocs, researchers and other employees in need of biostatistical skills within all Swedish universities. The course is geared towards life scientists wanting to be able to understand and use basic statistical and machine learning methods. It would also suit those already applying biostatistical methods but have never got a chance to truly understand the basic statistical concepts, such as the commonly misinterpreted p-value. **Fees** 2000 SEK includes lunches and coffee **Travel info** For travel information and hotel bookings see Travel Information page **Course credits** - Upon successful course completion, assessed based on active participation in all course session, we will issue a course certificate. - Please note that we are not able to provide any formal university credits (högskolepoäng). Many universities, however, recognize the attendance in our courses, and award 1.5 HPs, corresponding to 40h of studying. It is up to participants to clarify and arrange credit transfer with the relevant university department. **Selection criteria** - Due to limited space the course can accommodate maximum of 25 participants. If we receive more applications, participants will be selected based on several criteria. Selection criteria include correct entry requirements, motivation to attend the course as well as gender and geographical balance. - NBIS prioritises academic participants (students, staff, affiliated researchers) in Sweden. We can accept participants from industry and/or outside Sweden if we have seats available and the requirements criteria are met.NBIS/ELIXIR-SE Tools for Reproducible research
2024-04-22 to 2024-04-26 (5 days)
Deadline 2024-03-18
More info
This course aims to help researchers make their computational analysis more reproducible.One of the key principles of proper scientific procedure is the act of repeating an experiment or analysis and being able to reach similar conclusions. Published research based on computational analysis (e.g. bioinformatics or computational biology) have often suffered from incomplete method descriptions (e.g. list of used software versions); unavailable raw data; and incomplete, undocumented and/or unavailable code. This essentially prevents any possibility of reproducing the results of such studies. The term “reproducible research” has been used to describe the idea that a scientific publication should be distributed along with all the raw data and metadata used in the study, all the code and/or computational notebooks needed to produce results from the raw data, and the computational environment or a complete description thereof. Reproducible research not only leads to proper scientific conduct, but also enables other researchers to build upon previous work. Most importantly, the person who organizes their work with reproducibility in mind will quickly realize the immediate personal benefits: an organized and structured way of working. The person that most often has to reproduce your own analysis is your future self! **Application** This is an NBIS / Elixir course. The course is open for PhD students, postdocs, group leaders and core facility staff. International applications are welcome, but we will give approximately half of the participant slots to applicants from Swedish universities, due to the national role NBIS plays in Sweden. The only entry requirements for this course is a basic knowledge of Unix systems (i.e. being able to work on the command line) as well as at least a basic knowledge of either R or Python. Due to limited space the course can accommodate maximum of 20 participants. If we receive more applications, participants will be selected based on several criteria. Selection criteria include correct entry requirements, motivation to attend the course as well as gender and geographical balance. Please note that NBIS training events do not provide any formal university credits. The training content is estimated to correspond to a certain number of credits, however the estimated credits are just guidelines. If formal credits are crucial, the student needs to confer with the home department before submitting a course application in order to establish whether the course is valid for formal credits or not. By accepting to participate in the course, you agree to follow the [NBIS Training Code of Conduct](https://uppsala.instructure.com/courses/87979/pages/code-of-conduct). **Course fee** A course fee of 3000 SEK will be invoiced to accepted participants. This includes lunches, coffee and snacks, and course dinner. Please note that NBIS cannot invoice individualsProgramming Formalisms
2024-04-22 to 2024-04-26 (5 days)
Deadline 2024-04-18
Online
More info
This course aims to give life scientists, bioinformaticians, and other scientists with some experience in programming and scripting an understanding of the underlying principles of software development, design, and programming. The course aims to strengthen the understanding of more advanced programming concepts, ability to produce more reusable scripts through modular programming and to enable a better understanding of how to evaluate a script or programs performance.Data visualization in R
2024-04-16 to 2024-04-18 (3 days)
Deadline 2024-03-22
Stockholm
More info
This is a nation-wide course open for people who are interested in learning to plot using different packages in R. The course is organized by [NBIS](https://nbis.se/) (ELIXIR-SE). - This course aims to help researchers to visualize their data in different ways using R. This course will also aim to show researchers how they can make publication grade figures using R. - A part of this course is also about making interactive plots that the researchers can view and share in a web-server to make interactive visualizations of the data. **AUDIENCE** National course open for PhD students (prioritized), postdocs, researchers and other employees within all Swedish universities interested in learning to plot using different packages in R. **FEE** The fee for this on-site workshop is 2000 SEK to be paid by invoice to NBIS. Please note that NBIS cannot invoice individuals so we need your institutional invoicing address. The fee covers lunches, coffee and a course dinner. Those who accept the spot and then do not attend without prior notification will also be invoiced. Note that travel and accommodation is not included in the fee and must be arranged by the participants.A primer on cryo-EM data processing using cryoSPARC on BerzeLiUs
2024-04-15 to 2024-04-16 (2 days)
Deadline 2024-04-07
Online
More info
This course will introduce how to use Berzelius compute cluster for cryo-EM data processing. We will process the beta- galactosidase dataset, known from the Relion tutorials, but applying cryoSPARC on BerzeLiUs, as implemented by the PReSTO team.Introduction to bioinformatics using NGS data
2024-03-18 to 2024-03-22 (5 days)
Deadline 2024-02-05
Online
More info
An introductory workshop on applied bioinformatic next-generation sequence analyses run by the National Bioinformatic Infrastructure Sweden (NBIS) in partnership with National Genomics Infrastructure (NGI). **AUDIENCE** This workshop is open to PhD students, post-docs, and other researchers affiliated to Swedish academia and healthcare. We currently do not accept international applicants due to high volume of applicants. **FEE** The fee for this on-site workshop is 2000 SEK payed by invoice to NBIS. Please note that NBIS cannot invoice individuals so we need your institutional invoicing address. The fee covers lunches, coffee and a course dinner. Those who accept the spot and then do not attend without prior notification will also be invoiced. **Note that travel and accommodation is not included in the fee and must be arranged by the participants. ** **CREDITS & CERTIFICATE** Please note that NBIS training events do not provide any formal university credits. If formal credits are crucial, the student needs to confer with the home department before submitting a course application in order to establish whether the course is valid for formal credits or not. Attendees with full attendance and completion of tasks will be issued a certificate of participation indicating topics covered and duration of the workshop. **STUDENT SELECTION** Due to limited space the course can accommodate maximum of 30 participants. If we receive more applications, participants will be selected based on several criteria. Selection criteria include correct entry requirements, motivation to attend the workshop as well as gender and geographical balance. Priority is given to PhD scholars followed by other researchers. Due to the high volume of applications from Swedish academia, we currently do not accept international applicants.RNAseq data analysis
2024-03-11 to 2024-03-15 (5 days)
Deadline 2024-02-19
Uppsala
More info
This workshop will introduce the best practice bioinformatics methods for processing and analyses of RNA-seq data via a series of lectures and computer practicals.This workshop will introduce the best practice bioinformatics methods for processing and analyses of RNA-seq data via a series of online lectures and computer practicals. **Audience** National workshop open for PhD students, postdocs, researchers and other employees within Swedish academia. This course is run by the National Bioinformatics Infrastructure Sweden (NBIS). **Fee** 1800 SEK (for academic participants, please contact us for more information on the non-academic fee). Please note that NBIS cannot invoice individuals. The fee covers lunches, coffee and a course dinner. Those who accept the spot and then do not attend without prior notification will also be invoiced. **Note that travel and accommodation is not included in the fee and must be arranged by the participants. ** **Precourse material** Please read carefully the [Pre-course instructions](https://uppsala.instructure.com/courses/77082/pages/pre-course-instructions) material before the course start. If you have any problems with pre-course installations, please ask your questions in [Installation and pre-course related issues](https://uppsala.instructure.com/courses/77082/discussion_topics/238629). **Youtube videos** [RNASeq workshop videos](https://www.youtube.com/watch?v=VKhByCYa1R0&list=PLBsJUKzoJTHSGFT1f3WkU7tojmSLPvWVW)Single Cell RNAseq Data Analysis
2024-02-12 to 2024-02-16 (5 days)
Deadline 2024-01-17
Uppsala
More info
This workshop will introduce the best practice bioinformatics methods for processing and analyses of single cell RNA-seq data via a series of online lectures and computer practicals. The total course duration is 5 days, including the lectures and practical exercises that will be held on site in Stockholm. **Course fee**: This workshop has a fee of 2000kr and will be invoiced to the selected participants (Please note that NBIS cannot invoice individuals). Applications without complete invoice information will not be considered. Course fees cover all coffee breaks, all lunches and 1 course dinner. This is a national course. The course is open for PhD students, postdocs, group leaders and core facility staff within all Swedish universities. Even if we do accept application from other countries, we give priority to applicants from Swedish universities prior to applicants from industry and academics from other countries. Please note that NBIS training events do not provide any formal university credits. The training content is estimated to correspond to a certain number of credits, however the estimated credits are just guidelines. If formal credits are crucial, the student needs to confer with the home department before submitting a course application in order to establish whether the course is valid for formal credits or not. Practical exercises will be performed using either R or Python, so we only accept students that fulfil the entry requirements below. Due to limited space the course can accommodate maximum of 25 participants. If we receive more applications, participants will be selected based on several criteria. Selection criteria include correct entry requirements, motivation to attend the course as well as gender and geographical balance.DDLS Biomarker Discovery: from theory to real world examples
2023-12-06 to 2023-12-08 (3 days)
Deadline 2023-10-30
Stockholm
More info
The main purpose of this workshop is to provide a good overview of biomarkers and biomarker studies. This workshop will explore recent research, showcasing diverse biomarker applications within clinical trials. Methods employed to identify biomarkers through various omics datasets will be reviewed. Participants will engage in discussion on biomarker studies and data analysis exercises that encompass approaches like machine learning methods and other integrative omics strategies used in biomarker discovery.Snakemake BYOC (bring-your-own-code) workshop
2023-12-04 to 2023-12-06 (3 days)
Deadline 2023-10-29
Online
More info
As data analysis projects grow and change over time, it gets increasingly difficult to keep track of how the different parts of the data analysis fit together. Workflow management systems such as Snakemake Links to an external site. can be used to set up, perform and monitor defined sequences of computational tasks ("workflows"), thereby making data analyses reproducible and scalable. Snakemake was developed in the bioinformatics community and has some features that make it particularly well-suited for bioinformatic workflows. The NBIS Tools for reproducible research course is held twice a year and provides both an introduction to Snakemake and a tutorial on how to use it. This Snakemake BYOC (bring-your-own-code) workshop provides a follow-up to that introduction. Here, participants will get support from experienced bioinformaticians to A) convert their data analysis from a programming language such as Bash, R or Python into a Snakemake workflow, OR B) apply more advanced techniques to their existing Snakemake workflows. **Audience** Workshop open for PhD students (prioritized), postdocs, researchers and others who have previously participated in the [NBIS Tools for reproducible research course](https://uppsala.instructure.com/courses/82575) or with demonstrated experience in writing Snakemake workflows. **Fee** This online training event has no fee. However, if you confirm your participation but do not do so (no-show) you will be invoiced 2,000 SEK. Please note that NBIS cannot invoice individuals. By accepting to participate in the workshop, you will be agreeing to follow the NBIS Training Code of Conduct. Due to limited space, the workshop can accommodate a maximum of 12 participants. If we receive more applications, participants will be selected based on several criteria. Selection criteria include correct entry requirements, motivation to attend the workshop as well as gender- and geographical balance. This is a national workshop. The workshop is open for PhD students, postdocs, group leaders and core facility staff. We do accept applications from other countries, but give priority to applicants from Swedish universities prior to applicants from industry and academics from other countries. Please note that NBIS training events do not provide any formal university credits. The training content is estimated to correspond to a certain number of credits; however, the estimated credits are just guidelines. If formal credits are crucial, the student needs to confer with their home department before submitting a workshop application in order to establish whether the workshop is valid for formal credits or not.Programming Formalisms
2023-11-27 to 2023-12-01 (5 days)
Deadline 2023-11-24
Online
More info
This course aims to give life scientists, bioinformaticians, and other scientists with some experience in programming and scripting an understanding of the underlying principles of software development, design, and programming. The course aims to strengthen the understanding of more advanced programming concepts, ability to produce more reusable scripts through modular programming and to enable a better understanding of how to evaluate a script or programs performance.NBIS/ELIXIR-SE Tools for Reproducible research
2023-11-20 to 2023-11-24 (5 days)
Deadline 2023-10-20
More info
This course aims to help researchers make their computational analysis more reproducible.One of the key principles of proper scientific procedure is the act of repeating an experiment or analysis and being able to reach similar conclusions. Published research based on computational analysis (e.g. bioinformatics or computational biology) have often suffered from incomplete method descriptions (e.g. list of used software versions); unavailable raw data; and incomplete, undocumented and/or unavailable code. This essentially prevents any possibility of reproducing the results of such studies. The term “reproducible research” has been used to describe the idea that a scientific publication should be distributed along with all the raw data and metadata used in the study, all the code and/or computational notebooks needed to produce results from the raw data, and the computational environment or a complete description thereof. Reproducible research not only leads to proper scientific conduct, but also enables other researchers to build upon previous work. Most importantly, the person who organizes their work with reproducibility in mind will quickly realize the immediate personal benefits: an organized and structured way of working. The person that most often has to reproduce your own analysis is your future self! **Application** This is an NBIS / Elixir course. The course is open for PhD students, postdocs, group leaders and core facility staff. International applications are welcome, but we will give approximately half of the participant slots to applicants from Swedish universities, due to the national role NBIS plays in Sweden. The only entry requirements for this course is a basic knowledge of Unix systems (i.e. being able to work on the command line) as well as at least a basic knowledge of either R or Python. Due to limited space the course can accommodate maximum of 20 participants. If we receive more applications, participants will be selected based on several criteria. Selection criteria include correct entry requirements, motivation to attend the course as well as gender and geographical balance. Please note that NBIS training events do not provide any formal university credits. The training content is estimated to correspond to a certain number of credits, however the estimated credits are just guidelines. If formal credits are crucial, the student needs to confer with the home department before submitting a course application in order to establish whether the course is valid for formal credits or not. By accepting to participate in the course, you agree to follow the [NBIS Training Code of Conduct](https://uppsala.instructure.com/courses/87979/pages/code-of-conduct). **Course fee** A course fee of 3000 SEK will be invoiced to accepted participants. This includes lunches, coffee and snacks, and course dinner. Please note that NBIS cannot invoice individualsIntroduction to bioinformatics using NGS data
2023-11-13 to 2023-11-17 (5 days)
Deadline 2023-10-04
Uppsala
More info
An introductory workshop on applied bioinformatic next-generation sequence analyses run by the National Bioinformatic Infrastructure Sweden (NBIS) in partnership with National Genomics Infrastructure (NGI). **AUDIENCE** This workshop is open to PhD students, post-docs, and other researchers affiliated to Swedish academia and healthcare. We currently do not accept international applicants due to high volume of applicants. **FEE** The fee for this on-site workshop is 2000 SEK payed by invoice to NBIS. Please note that NBIS cannot invoice individuals so we need your institutional invoicing address. The fee covers lunches, coffee and a course dinner. Those who accept the spot and then do not attend without prior notification will also be invoiced. **Note that travel and accommodation is not included in the fee and must be arranged by the participants. ** **CREDITS & CERTIFICATE** Please note that NBIS training events do not provide any formal university credits. If formal credits are crucial, the student needs to confer with the home department before submitting a course application in order to establish whether the course is valid for formal credits or not. Attendees with full attendance and completion of tasks will be issued a certificate of participation indicating topics covered and duration of the workshop. **STUDENT SELECTION** Due to limited space the course can accommodate maximum of 30 participants. If we receive more applications, participants will be selected based on several criteria. Selection criteria include correct entry requirements, motivation to attend the workshop as well as gender and geographical balance. Priority is given to PhD scholars followed by other researchers. Due to the high volume of applications from Swedish academia, we currently do not accept international applicants.DDLS Population genomics in practice
2023-11-06 to 2023-11-10 (5 days)
Deadline 2023-09-30
Uppsala
More info
The aim of this workshop is to provide an introduction to commonly used methods in population genomics. As the focus of the course is on hands-on work, the topics have been designed to cover the fundamental analyses that are common in many population genomics studies. The course consists of lectures and exercises, with a focus on the practical aspects of analyses. Whereas lectures introduce some background theory, their primary aim is to set the stage for accompanying exercises.R Foundations for Life Scientists
2023-10-23 to 2023-10-27 (5 days)
Deadline 2023-09-20
Uppsala
More info
The course covers fundamental concepts of programming and software design focusing on programming in R. We will go through various aspects of R scripting emphasizing the parts useful for life scientists. After introductory lectures on good programming practices, basic software design theory and a brief overview of R, we will delve into programming.Python programming with applications to bioinformatics
2023-10-09 to 2023-10-13 (5 days)
Deadline 2023-09-08
Uppsala, Umeå
More info
This course provides a practical introduction to the writing of [Python](https://www.python.org/) programs for the complete novice. Participants are lead through the core aspects of Python illustrated by a series of example programs. Upon completion of the course, attentive participants will be able to write simple Python programs from scratch and to customize more complex code to fit their needs. - The course is suitable for complete beginners and assumes no prior programming experience (beyond the ability to use a text editor). - A very basic knowledge of UNIX would be an advantage, such as navigating through folders and issuing commands at a shell prompt. We will not teach Unix in detail: Other course are available at SciLifeLab for it. Before the first lecture, we require you to follow the steps detailed in the [pre-course material](https://uppsala.instructure.com/courses/85913/pages/pre-course-material). **Audience** Course open to PhD students, postdocs, and other researchers. Note that priority is given to Swedish academia. **Fee** A course fee of 3000 SEK will be invoiced to accepted participants. This includes lunches, coffee and snacks, and course dinner. Please note that NBIS cannot invoice individuals By participating you will be agreeing to the [NBIS Code of Conduct](https://uppsala.instructure.com/courses/85913/pages/nbis-training-code-of-conduct?module_item_id=836091).Epigenomics Data Analysis: from Bulk to Single Cell
2023-09-18 to 2023-09-22 (5 days)
Deadline 2023-09-04
Online
More info
The aim of this workshop is to introduce best practice bioinformatics methods for processing, analyses and integration of epigenomics data. The online teaching includes lectures, programming tutorials and interactive group sessions. This workshop is run by the National Bioinformatics Infrastructure Sweden (NBIS). **Audience** Course open to PhD students, postdocs, and other researchers. Note that priority is given to Swedish academia. **Fee** This online training event has no fee. However, if you confirm your participation but do not do so (no-show) you will be invoiced 2000 SEK. Please note that NBIS cannot invoice individuals. By accepting to participate in the course, you will be agreeing to follow the [NBIS Training Code of Conduct](https://uppsala.instructure.com/courses/48087/pages/nbis-training-code-of-conduct). We will issue a course certificate upon a successful course completion, assessed by active participation in all course sessions (lectures, computer practicals, group discussion etc.). Unfortunately we are **not** able to warrant any university credits (högskolepoäng). Many universities however, recognize the attendance in our courses and award 1.5 HPs, corresponding to a 40 h of studying. It is up to participants to clarify and arrange credit transfer with the relevant university department.ELIXIR-GOBLET Train-the-Trainer
2023-09-13 to 2023-09-15 (3 days)
Deadline 2023-08-21
Uppsala
More info
This course offers guidance, ideas and tips for designing training/teaching, development and delivery on training activities, all based on research-driven educational principles. This course will cover 4 main topics: - Learning principles and how they apply to training and teaching - Design and plan session, course, materials - Teaching techniques to enhance learner engagement and participation - Assessment and feedback in training and teaching Note! The course is highly interactive and hence it is important that you, as a participant, actively contribute to all sessions and elements of the course.RaukR, Advanced R for Bioinformatics
2023-06-11 to 2023-06-22 (12 days)
Visby
More info
In Life Sciences and Bioinformatics, the R programming language is pivotal for data transformation, statistical analyses, and crafting publication-ready visualizations. This workshop goes beyond the basics, offering participants a comprehensive understanding of the R ecosystem. We explore best coding practices, code profiling, delve into data wrangling intricacies, emphasize reproducible research and hands-on development of web apps using R. **Course materials** Course materials will be made available at the beginning of the workshop and will remain open and publicly accessible online for at least a year. You can check out the materials from 2023. **Sessions** Our daily schedule begins with a morning session from 08:30 to 12:30, starting with breakfast from 08:30 to 09:00 and a 30-minute break at 10:30. Lunchtime is from 12:30 to 13:30. The afternoon session follows, running from 13:30 to 17:00, with a 30-minute coffee break at 15:00. Please note that due to varying time zones, online guest lectures might occur after 17:00. Throughout the majority of sessions, our instructors and teaching assistants will be available to aid you with practical exercises and answer any queries you may have. **Selection** We can accomodate ~42 participants. Selection criteria include correct entry requirements, motivation to attend the workshop as well as gender and geographical balance. We do accept international applicants, but applicants affiliated to a Swedish institution are prioritized. Once the registration period concludes, we will review your application and notify you of our decision. If accepted, you will have three working days to confirm your participation. Failure to do so would imply your inability to attend, and we will proceed accordingly. Once you confirmed, our course administrator will proceed with invoicing. **Fee** The fee for academic participants is 8000 SEK subsidized by academic grants. Fee for non-academic participants is 16 000 SEK. **Warning** If you register and are admitted but fail to attend without a valid reason (sickness or urgent family matter), you will still be liable for the entire fee. **More info about the fee** _Included in the fee_ - Participation in lectures and workshops - Mingle reception with snacks and drinks - Daily breakfast/coffee, lunch and afternoon coffee during the workshop - One official course dinner - Surprise social activities _Not included in the fee_ - Accomodation - Travel to and from Visby - Daily dinnersNBIS/ELIXIR-SE Tools for Reproducible research
2023-04-24 to 2023-04-28 (5 days)
Online
More info
This course aims to help researchers make their computational analysis more reproducible.One of the key principles of proper scientific procedure is the act of repeating an experiment or analysis and being able to reach similar conclusions. Published research based on computational analysis (e.g. bioinformatics or computational biology) have often suffered from incomplete method descriptions (e.g. list of used software versions); unavailable raw data; and incomplete, undocumented and/or unavailable code. This essentially prevents any possibility of reproducing the results of such studies. The term “reproducible research” has been used to describe the idea that a scientific publication should be distributed along with all the raw data and metadata used in the study, all the code and/or computational notebooks needed to produce results from the raw data, and the computational environment or a complete description thereof. Reproducible research not only leads to proper scientific conduct, but also enables other researchers to build upon previous work. Most importantly, the person who organizes their work with reproducibility in mind will quickly realize the immediate personal benefits: an organized and structured way of working. The person that most often has to reproduce your own analysis is your future self! **Application** This is an NBIS / Elixir course. The course is open for PhD students, postdocs, group leaders and core facility staff. International applications are welcome, but we will give approximately half of the participant slots to applicants from Swedish universities, due to the national role NBIS plays in Sweden. The only entry requirements for this course is a basic knowledge of Unix systems (i.e. being able to work on the command line) as well as at least a basic knowledge of either R or Python. Due to limited space the course can accommodate maximum of 20 participants. If we receive more applications, participants will be selected based on several criteria. Selection criteria include correct entry requirements, motivation to attend the course as well as gender and geographical balance. Please note that NBIS training events do not provide any formal university credits. The training content is estimated to correspond to a certain number of credits, however the estimated credits are just guidelines. If formal credits are crucial, the student needs to confer with the home department before submitting a course application in order to establish whether the course is valid for formal credits or not. By accepting to participate in the course, you agree to follow the [NBIS Training Code of Conduct](https://uppsala.instructure.com/courses/87979/pages/code-of-conduct). **Course fee** A course fee of 3000 SEK will be invoiced to accepted participants. This includes lunches, coffee and snacks, and course dinner. Please note that NBIS cannot invoice individualsIntroduction to Biostatistics and Machine Learning
2023-04-24 to 2023-04-28 (5 days)
Uppsala
More info
National course open for PhD students, postdocs, researchers and other employees in need of biostatistical skills within all Swedish universities. The course is geared towards life scientists wanting to be able to understand and use basic statistical and machine learning methods. It would also suit those already applying biostatistical methods but have never got a chance to truly understand the basic statistical concepts, such as the commonly misinterpreted p-value. **Fees** 2000 SEK includes lunches and coffee **Travel info** For travel information and hotel bookings see Travel Information page **Course credits** - Upon successful course completion, assessed based on active participation in all course session, we will issue a course certificate. - Please note that we are not able to provide any formal university credits (högskolepoäng). Many universities, however, recognize the attendance in our courses, and award 1.5 HPs, corresponding to 40h of studying. It is up to participants to clarify and arrange credit transfer with the relevant university department. **Selection criteria** - Due to limited space the course can accommodate maximum of 25 participants. If we receive more applications, participants will be selected based on several criteria. Selection criteria include correct entry requirements, motivation to attend the course as well as gender and geographical balance. - NBIS prioritises academic participants (students, staff, affiliated researchers) in Sweden. We can accept participants from industry and/or outside Sweden if we have seats available and the requirements criteria are met.Introduction to Data Management Practices
2023-04-18 to 2023-04-20 (3 days)
Uppsala
More info
This course will introduce important aspects of Research Data Management through a series of lectures and hands-on computer exercises. The course is intended for researchers that want to take the first steps towards a more systematic and reproducible approach to analysing and managing research data. **Application instructions** National course open for PhD students, postdocs, researchers and other employees within all Swedish universities. The course is geared towards life scientists wanting to take the first steps towards a more systematic and reproducible approach to analysing and managing research data. **Fee** We charge a fee for onsite course occasions, to be paid by invoice to NBIS. This includes lunches, coffee and snacks. _Please note that NBIS **cannot** invoice individuals._Data visualization in R
2023-04-17 to 2023-04-19 (3 days)
Lund
More info
This is a nation-wide course open for people who are interested in learning to plot using different packages in R. The course is organized by [NBIS](https://nbis.se/) (ELIXIR-SE). - This course aims to help researchers to visualize their data in different ways using R. This course will also aim to show researchers how they can make publication grade figures using R. - A part of this course is also about making interactive plots that the researchers can view and share in a web-server to make interactive visualizations of the data. **AUDIENCE** National course open for PhD students (prioritized), postdocs, researchers and other employees within all Swedish universities interested in learning to plot using different packages in R. **FEE** The fee for this on-site workshop is 2000 SEK to be paid by invoice to NBIS. Please note that NBIS cannot invoice individuals so we need your institutional invoicing address. The fee covers lunches, coffee and a course dinner. Those who accept the spot and then do not attend without prior notification will also be invoiced. Note that travel and accommodation is not included in the fee and must be arranged by the participants.Neural Networks and Deep Learning
2023-03-20 to 2023-03-24 (5 days)
Uppsala
More info
This course will give an introduction to the concept of Neural Networks (NN) and Deep Learning. Topics covered will include: NN building blocks, including concepts such as neurons, activation functions, loss functions, gradient descent and back-propagation; Convolutional Neural Networks; Recursive Neural Networks; Autoencoders; and best practices when designing NNs,RNAseq data analysis
2023-03-13 to 2023-03-16 (4 days)
Uppsala
More info
This workshop will introduce the best practice bioinformatics methods for processing and analyses of RNA-seq data via a series of lectures and computer practicals.This workshop will introduce the best practice bioinformatics methods for processing and analyses of RNA-seq data via a series of online lectures and computer practicals. **Audience** National workshop open for PhD students, postdocs, researchers and other employees within Swedish academia. This course is run by the National Bioinformatics Infrastructure Sweden (NBIS). **Fee** 1800 SEK (for academic participants, please contact us for more information on the non-academic fee). Please note that NBIS cannot invoice individuals. The fee covers lunches, coffee and a course dinner. Those who accept the spot and then do not attend without prior notification will also be invoiced. **Note that travel and accommodation is not included in the fee and must be arranged by the participants. ** **Precourse material** Please read carefully the [Pre-course instructions](https://uppsala.instructure.com/courses/77082/pages/pre-course-instructions) material before the course start. If you have any problems with pre-course installations, please ask your questions in [Installation and pre-course related issues](https://uppsala.instructure.com/courses/77082/discussion_topics/238629). **Youtube videos** [RNASeq workshop videos](https://www.youtube.com/watch?v=VKhByCYa1R0&list=PLBsJUKzoJTHSGFT1f3WkU7tojmSLPvWVW)Omics Integration and Systems Biology
2023-02-08 to 2023-02-10 (3 days)
Online
More info
**Application** Course open for PhD students, postdocs, group leaders and core facility staff from Sweden and European institutions looking for an introduction to multi-omics integration and systems biology approaches. Please note that NBIS training events do not provide any formal university credits. If formal credits are crucial, the student needs to confer with the home department before submitting a course application in order to establish whether the course is valid for formal credits or not. [Click here](https://forms.gle/Qet7uJnsJqQdtY2h7) if you would like to be notified of the next course instance. **Fee** This workshop has a fee of 3000kr and will be invoiced to the selected participants (Please note that NBIS cannot invoice individuals). Applications without complete invoice information will not be considered. Course fees cover all coffee breaks, all lunches and 1 course dinner.Introduction to bioinformatics using NGS data
2023-02-06 to 2023-02-10 (5 days)
Uppsala
More info
An introductory workshop on applied bioinformatic next-generation sequence analyses run by the National Bioinformatic Infrastructure Sweden (NBIS) in partnership with National Genomics Infrastructure (NGI). **AUDIENCE** This workshop is open to PhD students, post-docs, and other researchers affiliated to Swedish academia and healthcare. We currently do not accept international applicants due to high volume of applicants. **FEE** The fee for this on-site workshop is 2000 SEK payed by invoice to NBIS. Please note that NBIS cannot invoice individuals so we need your institutional invoicing address. The fee covers lunches, coffee and a course dinner. Those who accept the spot and then do not attend without prior notification will also be invoiced. **Note that travel and accommodation is not included in the fee and must be arranged by the participants. ** **CREDITS & CERTIFICATE** Please note that NBIS training events do not provide any formal university credits. If formal credits are crucial, the student needs to confer with the home department before submitting a course application in order to establish whether the course is valid for formal credits or not. Attendees with full attendance and completion of tasks will be issued a certificate of participation indicating topics covered and duration of the workshop. **STUDENT SELECTION** Due to limited space the course can accommodate maximum of 30 participants. If we receive more applications, participants will be selected based on several criteria. Selection criteria include correct entry requirements, motivation to attend the workshop as well as gender and geographical balance. Priority is given to PhD scholars followed by other researchers. Due to the high volume of applications from Swedish academia, we currently do not accept international applicants.Single Cell RNAseq Data Analysis
2023-01-30 to 2023-02-03 (5 days)
Solna
More info
This workshop will introduce the best practice bioinformatics methods for processing and analyses of single cell RNA-seq data via a series of online lectures and computer practicals. The total course duration is 5 days, including the lectures and practical exercises that will be held on site in Stockholm. **Course fee**: This workshop has a fee of 2000kr and will be invoiced to the selected participants (Please note that NBIS cannot invoice individuals). Applications without complete invoice information will not be considered. Course fees cover all coffee breaks, all lunches and 1 course dinner. This is a national course. The course is open for PhD students, postdocs, group leaders and core facility staff within all Swedish universities. Even if we do accept application from other countries, we give priority to applicants from Swedish universities prior to applicants from industry and academics from other countries. Please note that NBIS training events do not provide any formal university credits. The training content is estimated to correspond to a certain number of credits, however the estimated credits are just guidelines. If formal credits are crucial, the student needs to confer with the home department before submitting a course application in order to establish whether the course is valid for formal credits or not. Practical exercises will be performed using either R or Python, so we only accept students that fulfil the entry requirements below. Due to limited space the course can accommodate maximum of 25 participants. If we receive more applications, participants will be selected based on several criteria. Selection criteria include correct entry requirements, motivation to attend the course as well as gender and geographical balance.Tools for Reproducible Research
2022-11-21 to 2022-11-25 (5 days)
Online
More info
One of the key principles of proper scientific procedure is the act of repeating an experiment or analysis and being able to reach similar conclusions. Published research based on computational analysis, e.g. bioinformatics or computational biology, have often suffered from incomplete method descriptions (e.g. list of used software versions); unavailable raw data; and incomplete, undocumented and/or unavailable code. This essentially prevents any possibility of attempting to reproduce the results of such studies. The term “reproducible research” has been used to describe the idea that a scientific publication based on computational analysis should be distributed along with all the raw data and metadata used in the study, all the code and/or computational notebooks needed to produce results from the raw data, and the computational environment or a complete description thereof. Reproducible research not only leads to proper scientific conduct but also provides other researchers the access to build upon previous work. Most importantly, the person setting up a reproducible research project will quickly realize the immediate personal benefits: an organized and structured way of working. The person that most often has to reproduce your own analysis is your future self!Programming Formalisms
2022-10-24 to 2022-10-28 (5 days)
Online
More info
This course aims to give life scientists, bioinformaticians, and other scientists with some experience in programming and scripting an understanding of the underlying principles of software development, design, and programming. The course aims to strengthen the understanding of more advanced programming concepts, ability to produce more reusable scripts through modular programming and to enable a better understanding of how to evaluate a script or programs performance.Epigenomics Data Analysis: from Bulk to Single Cell
2022-10-24 to 2022-10-28 (5 days)
Online
More info
The aim of this workshop is to introduce best practice bioinformatics methods for processing, analyses and integration of epigenomics data. The online teaching includes lectures, programming tutorials and interactive group sessions. This workshop is run by the National Bioinformatics Infrastructure Sweden (NBIS). **Audience** Course open to PhD students, postdocs, and other researchers. Note that priority is given to Swedish academia. **Fee** This online training event has no fee. However, if you confirm your participation but do not do so (no-show) you will be invoiced 2000 SEK. Please note that NBIS cannot invoice individuals. By accepting to participate in the course, you will be agreeing to follow the [NBIS Training Code of Conduct](https://uppsala.instructure.com/courses/48087/pages/nbis-training-code-of-conduct). We will issue a course certificate upon a successful course completion, assessed by active participation in all course sessions (lectures, computer practicals, group discussion etc.). Unfortunately we are **not** able to warrant any university credits (högskolepoäng). Many universities however, recognize the attendance in our courses and award 1.5 HPs, corresponding to a 40 h of studying. It is up to participants to clarify and arrange credit transfer with the relevant university department.Introduction to Data Management Practices
2022-10-11 to 2022-10-13 (3 days)
Solna
More info
This course will introduce important aspects of Research Data Management through a series of lectures and hands-on computer exercises. The course is intended for researchers that want to take the first steps towards a more systematic and reproducible approach to analysing and managing research data. **Application instructions** National course open for PhD students, postdocs, researchers and other employees within all Swedish universities. The course is geared towards life scientists wanting to take the first steps towards a more systematic and reproducible approach to analysing and managing research data. **Fee** We charge a fee for onsite course occasions, to be paid by invoice to NBIS. This includes lunches, coffee and snacks. _Please note that NBIS **cannot** invoice individuals._Python programming with applications to bioinformatics
2022-10-10 to 2022-10-14 (5 days)
Online
More info
This course provides a practical introduction to the writing of [Python](https://www.python.org/) programs for the complete novice. Participants are lead through the core aspects of Python illustrated by a series of example programs. Upon completion of the course, attentive participants will be able to write simple Python programs from scratch and to customize more complex code to fit their needs. - The course is suitable for complete beginners and assumes no prior programming experience (beyond the ability to use a text editor). - A very basic knowledge of UNIX would be an advantage, such as navigating through folders and issuing commands at a shell prompt. We will not teach Unix in detail: Other course are available at SciLifeLab for it. Before the first lecture, we require you to follow the steps detailed in the [pre-course material](https://uppsala.instructure.com/courses/85913/pages/pre-course-material). **Audience** Course open to PhD students, postdocs, and other researchers. Note that priority is given to Swedish academia. **Fee** A course fee of 3000 SEK will be invoiced to accepted participants. This includes lunches, coffee and snacks, and course dinner. Please note that NBIS cannot invoice individuals By participating you will be agreeing to the [NBIS Code of Conduct](https://uppsala.instructure.com/courses/85913/pages/nbis-training-code-of-conduct?module_item_id=836091).Introduction to bioinformatics using NGS data
2022-09-26 to 2022-09-30 (5 days)
Uppsala
More info
An introductory workshop on applied bioinformatic next-generation sequence analyses run by the National Bioinformatic Infrastructure Sweden (NBIS) in partnership with National Genomics Infrastructure (NGI). **AUDIENCE** This workshop is open to PhD students, post-docs, and other researchers affiliated to Swedish academia and healthcare. We currently do not accept international applicants due to high volume of applicants. **FEE** The fee for this on-site workshop is 2000 SEK payed by invoice to NBIS. Please note that NBIS cannot invoice individuals so we need your institutional invoicing address. The fee covers lunches, coffee and a course dinner. Those who accept the spot and then do not attend without prior notification will also be invoiced. **Note that travel and accommodation is not included in the fee and must be arranged by the participants. ** **CREDITS & CERTIFICATE** Please note that NBIS training events do not provide any formal university credits. If formal credits are crucial, the student needs to confer with the home department before submitting a course application in order to establish whether the course is valid for formal credits or not. Attendees with full attendance and completion of tasks will be issued a certificate of participation indicating topics covered and duration of the workshop. **STUDENT SELECTION** Due to limited space the course can accommodate maximum of 30 participants. If we receive more applications, participants will be selected based on several criteria. Selection criteria include correct entry requirements, motivation to attend the workshop as well as gender and geographical balance. Priority is given to PhD scholars followed by other researchers. Due to the high volume of applications from Swedish academia, we currently do not accept international applicants.Introduction to Biostatistics and Machine Learning
2022-09-12 to 2022-09-16 (5 days)
Uppsala
More info
National course open for PhD students, postdocs, researchers and other employees in need of biostatistical skills within all Swedish universities. The course is geared towards life scientists wanting to be able to understand and use basic statistical and machine learning methods. It would also suit those already applying biostatistical methods but have never got a chance to truly understand the basic statistical concepts, such as the commonly misinterpreted p-value. **Fees** 2000 SEK includes lunches and coffee **Travel info** For travel information and hotel bookings see Travel Information page **Course credits** - Upon successful course completion, assessed based on active participation in all course session, we will issue a course certificate. - Please note that we are not able to provide any formal university credits (högskolepoäng). Many universities, however, recognize the attendance in our courses, and award 1.5 HPs, corresponding to 40h of studying. It is up to participants to clarify and arrange credit transfer with the relevant university department. **Selection criteria** - Due to limited space the course can accommodate maximum of 25 participants. If we receive more applications, participants will be selected based on several criteria. Selection criteria include correct entry requirements, motivation to attend the course as well as gender and geographical balance. - NBIS prioritises academic participants (students, staff, affiliated researchers) in Sweden. We can accept participants from industry and/or outside Sweden if we have seats available and the requirements criteria are met.Snakemake BYOC (bring-your-own-code) workshop
2022-08-31 to 2022-09-02 (3 days)
Online
More info
As data analysis projects grow and change over time, it gets increasingly difficult to keep track of how the different parts of the data analysis fit together. Workflow management systems such as Snakemake Links to an external site. can be used to set up, perform and monitor defined sequences of computational tasks ("workflows"), thereby making data analyses reproducible and scalable. Snakemake was developed in the bioinformatics community and has some features that make it particularly well-suited for bioinformatic workflows. The NBIS Tools for reproducible research course is held twice a year and provides both an introduction to Snakemake and a tutorial on how to use it. This Snakemake BYOC (bring-your-own-code) workshop provides a follow-up to that introduction. Here, participants will get support from experienced bioinformaticians to A) convert their data analysis from a programming language such as Bash, R or Python into a Snakemake workflow, OR B) apply more advanced techniques to their existing Snakemake workflows. **Audience** Workshop open for PhD students (prioritized), postdocs, researchers and others who have previously participated in the [NBIS Tools for reproducible research course](https://uppsala.instructure.com/courses/82575) or with demonstrated experience in writing Snakemake workflows. **Fee** This online training event has no fee. However, if you confirm your participation but do not do so (no-show) you will be invoiced 2,000 SEK. Please note that NBIS cannot invoice individuals. By accepting to participate in the workshop, you will be agreeing to follow the NBIS Training Code of Conduct. Due to limited space, the workshop can accommodate a maximum of 12 participants. If we receive more applications, participants will be selected based on several criteria. Selection criteria include correct entry requirements, motivation to attend the workshop as well as gender- and geographical balance. This is a national workshop. The workshop is open for PhD students, postdocs, group leaders and core facility staff. We do accept applications from other countries, but give priority to applicants from Swedish universities prior to applicants from industry and academics from other countries. Please note that NBIS training events do not provide any formal university credits. The training content is estimated to correspond to a certain number of credits; however, the estimated credits are just guidelines. If formal credits are crucial, the student needs to confer with their home department before submitting a workshop application in order to establish whether the workshop is valid for formal credits or not.Spatial omics data analysis
RaukR, Advanced R for Bioinformatics
2022-06-13 to 2022-06-17 (5 days)
Online
More info
In Life Sciences and Bioinformatics, the R programming language is pivotal for data transformation, statistical analyses, and crafting publication-ready visualizations. This workshop goes beyond the basics, offering participants a comprehensive understanding of the R ecosystem. We explore best coding practices, code profiling, delve into data wrangling intricacies, emphasize reproducible research and hands-on development of web apps using R. **Course materials** Course materials will be made available at the beginning of the workshop and will remain open and publicly accessible online for at least a year. You can check out the materials from 2023. **Sessions** Our daily schedule begins with a morning session from 08:30 to 12:30, starting with breakfast from 08:30 to 09:00 and a 30-minute break at 10:30. Lunchtime is from 12:30 to 13:30. The afternoon session follows, running from 13:30 to 17:00, with a 30-minute coffee break at 15:00. Please note that due to varying time zones, online guest lectures might occur after 17:00. Throughout the majority of sessions, our instructors and teaching assistants will be available to aid you with practical exercises and answer any queries you may have. **Selection** We can accomodate ~42 participants. Selection criteria include correct entry requirements, motivation to attend the workshop as well as gender and geographical balance. We do accept international applicants, but applicants affiliated to a Swedish institution are prioritized. Once the registration period concludes, we will review your application and notify you of our decision. If accepted, you will have three working days to confirm your participation. Failure to do so would imply your inability to attend, and we will proceed accordingly. Once you confirmed, our course administrator will proceed with invoicing. **Fee** The fee for academic participants is 8000 SEK subsidized by academic grants. Fee for non-academic participants is 16 000 SEK. **Warning** If you register and are admitted but fail to attend without a valid reason (sickness or urgent family matter), you will still be liable for the entire fee. **More info about the fee** _Included in the fee_ - Participation in lectures and workshops - Mingle reception with snacks and drinks - Daily breakfast/coffee, lunch and afternoon coffee during the workshop - One official course dinner - Surprise social activities _Not included in the fee_ - Accomodation - Travel to and from Visby - Daily dinnersELIXIR-GOBLET Train-the-Trainer
2022-05-10 to 2022-05-13 (4 days)
Online
More info
This course offers guidance, ideas and tips for designing training/teaching, development and delivery on training activities, all based on research-driven educational principles. This course will cover 4 main topics: - Learning principles and how they apply to training and teaching - Design and plan session, course, materials - Teaching techniques to enhance learner engagement and participation - Assessment and feedback in training and teaching Note! The course is highly interactive and hence it is important that you, as a participant, actively contribute to all sessions and elements of the course.Data visualization in R
2022-04-27 to 2022-04-29 (3 days)
Lund
More info
This is a nation-wide course open for people who are interested in learning to plot using different packages in R. The course is organized by [NBIS](https://nbis.se/) (ELIXIR-SE). - This course aims to help researchers to visualize their data in different ways using R. This course will also aim to show researchers how they can make publication grade figures using R. - A part of this course is also about making interactive plots that the researchers can view and share in a web-server to make interactive visualizations of the data. **AUDIENCE** National course open for PhD students (prioritized), postdocs, researchers and other employees within all Swedish universities interested in learning to plot using different packages in R. **FEE** The fee for this on-site workshop is 2000 SEK to be paid by invoice to NBIS. Please note that NBIS cannot invoice individuals so we need your institutional invoicing address. The fee covers lunches, coffee and a course dinner. Those who accept the spot and then do not attend without prior notification will also be invoiced. Note that travel and accommodation is not included in the fee and must be arranged by the participants.NBIS/ELIXIR-SE Tools for Reproducible research
2022-04-25 to 2022-04-29 (5 days)
Online
More info
This course aims to help researchers make their computational analysis more reproducible.One of the key principles of proper scientific procedure is the act of repeating an experiment or analysis and being able to reach similar conclusions. Published research based on computational analysis (e.g. bioinformatics or computational biology) have often suffered from incomplete method descriptions (e.g. list of used software versions); unavailable raw data; and incomplete, undocumented and/or unavailable code. This essentially prevents any possibility of reproducing the results of such studies. The term “reproducible research” has been used to describe the idea that a scientific publication should be distributed along with all the raw data and metadata used in the study, all the code and/or computational notebooks needed to produce results from the raw data, and the computational environment or a complete description thereof. Reproducible research not only leads to proper scientific conduct, but also enables other researchers to build upon previous work. Most importantly, the person who organizes their work with reproducibility in mind will quickly realize the immediate personal benefits: an organized and structured way of working. The person that most often has to reproduce your own analysis is your future self! **Application** This is an NBIS / Elixir course. The course is open for PhD students, postdocs, group leaders and core facility staff. International applications are welcome, but we will give approximately half of the participant slots to applicants from Swedish universities, due to the national role NBIS plays in Sweden. The only entry requirements for this course is a basic knowledge of Unix systems (i.e. being able to work on the command line) as well as at least a basic knowledge of either R or Python. Due to limited space the course can accommodate maximum of 20 participants. If we receive more applications, participants will be selected based on several criteria. Selection criteria include correct entry requirements, motivation to attend the course as well as gender and geographical balance. Please note that NBIS training events do not provide any formal university credits. The training content is estimated to correspond to a certain number of credits, however the estimated credits are just guidelines. If formal credits are crucial, the student needs to confer with the home department before submitting a course application in order to establish whether the course is valid for formal credits or not. By accepting to participate in the course, you agree to follow the [NBIS Training Code of Conduct](https://uppsala.instructure.com/courses/87979/pages/code-of-conduct). **Course fee** A course fee of 3000 SEK will be invoiced to accepted participants. This includes lunches, coffee and snacks, and course dinner. Please note that NBIS cannot invoice individualsIntroduction to Data Management Practices
2022-04-05 to 2022-04-07 (3 days)
Uppsala
More info
This course will introduce important aspects of Research Data Management through a series of lectures and hands-on computer exercises. The course is intended for researchers that want to take the first steps towards a more systematic and reproducible approach to analysing and managing research data. **Application instructions** National course open for PhD students, postdocs, researchers and other employees within all Swedish universities. The course is geared towards life scientists wanting to take the first steps towards a more systematic and reproducible approach to analysing and managing research data. **Fee** We charge a fee for onsite course occasions, to be paid by invoice to NBIS. This includes lunches, coffee and snacks. _Please note that NBIS **cannot** invoice individuals._Introduction to bioinformatics using NGS data
2022-03-28 to 2022-04-01 (5 days)
Online
More info
An introductory workshop on applied bioinformatic next-generation sequence analyses run by the National Bioinformatic Infrastructure Sweden (NBIS) in partnership with National Genomics Infrastructure (NGI). **AUDIENCE** This workshop is open to PhD students, post-docs, and other researchers affiliated to Swedish academia and healthcare. We currently do not accept international applicants due to high volume of applicants. **FEE** The fee for this on-site workshop is 2000 SEK payed by invoice to NBIS. Please note that NBIS cannot invoice individuals so we need your institutional invoicing address. The fee covers lunches, coffee and a course dinner. Those who accept the spot and then do not attend without prior notification will also be invoiced. **Note that travel and accommodation is not included in the fee and must be arranged by the participants. ** **CREDITS & CERTIFICATE** Please note that NBIS training events do not provide any formal university credits. If formal credits are crucial, the student needs to confer with the home department before submitting a course application in order to establish whether the course is valid for formal credits or not. Attendees with full attendance and completion of tasks will be issued a certificate of participation indicating topics covered and duration of the workshop. **STUDENT SELECTION** Due to limited space the course can accommodate maximum of 30 participants. If we receive more applications, participants will be selected based on several criteria. Selection criteria include correct entry requirements, motivation to attend the workshop as well as gender and geographical balance. Priority is given to PhD scholars followed by other researchers. Due to the high volume of applications from Swedish academia, we currently do not accept international applicants.Single Cell RNAseq Data Analysis
2022-02-02 to 2022-02-04 (3 days)
Solna
More info
This workshop will introduce the best practice bioinformatics methods for processing and analyses of single cell RNA-seq data via a series of online lectures and computer practicals. The total course duration is 5 days, including the lectures and practical exercises that will be held on site in Stockholm. **Course fee**: This workshop has a fee of 2000kr and will be invoiced to the selected participants (Please note that NBIS cannot invoice individuals). Applications without complete invoice information will not be considered. Course fees cover all coffee breaks, all lunches and 1 course dinner. This is a national course. The course is open for PhD students, postdocs, group leaders and core facility staff within all Swedish universities. Even if we do accept application from other countries, we give priority to applicants from Swedish universities prior to applicants from industry and academics from other countries. Please note that NBIS training events do not provide any formal university credits. The training content is estimated to correspond to a certain number of credits, however the estimated credits are just guidelines. If formal credits are crucial, the student needs to confer with the home department before submitting a course application in order to establish whether the course is valid for formal credits or not. Practical exercises will be performed using either R or Python, so we only accept students that fulfil the entry requirements below. Due to limited space the course can accommodate maximum of 25 participants. If we receive more applications, participants will be selected based on several criteria. Selection criteria include correct entry requirements, motivation to attend the course as well as gender and geographical balance.Neural Networks and Deep Learning
2022-01-17 to 2022-01-21 (5 days)
Uppsala
More info
This course will give an introduction to the concept of Neural Networks (NN) and Deep Learning. Topics covered will include: NN building blocks, including concepts such as neurons, activation functions, loss functions, gradient descent and back-propagation; Convolutional Neural Networks; Recursive Neural Networks; Autoencoders; and best practices when designing NNs,FAIR principles in life science research practice
2021-12-09 to 2021-12-09 (1 days)
Online
More info
This online workshop will showcase how to put the FAIR principles into practice and is specifically designed to cater to life science researchers at all career stages. It is organised by SciLifeLab Data Centre and NBIS and include international speakers, presenters from the SciLifeLab community and optional hands-on exercises guided by experts from NBIS and SciLifeLab Data Centre.Introduction to bioinformatics using NGS data
2021-11-22 to 2021-11-26 (5 days)
Online
More info
An introductory workshop on applied bioinformatic next-generation sequence analyses run by the National Bioinformatic Infrastructure Sweden (NBIS) in partnership with National Genomics Infrastructure (NGI). **AUDIENCE** This workshop is open to PhD students, post-docs, and other researchers affiliated to Swedish academia and healthcare. We currently do not accept international applicants due to high volume of applicants. **FEE** The fee for this on-site workshop is 2000 SEK payed by invoice to NBIS. Please note that NBIS cannot invoice individuals so we need your institutional invoicing address. The fee covers lunches, coffee and a course dinner. Those who accept the spot and then do not attend without prior notification will also be invoiced. **Note that travel and accommodation is not included in the fee and must be arranged by the participants. ** **CREDITS & CERTIFICATE** Please note that NBIS training events do not provide any formal university credits. If formal credits are crucial, the student needs to confer with the home department before submitting a course application in order to establish whether the course is valid for formal credits or not. Attendees with full attendance and completion of tasks will be issued a certificate of participation indicating topics covered and duration of the workshop. **STUDENT SELECTION** Due to limited space the course can accommodate maximum of 30 participants. If we receive more applications, participants will be selected based on several criteria. Selection criteria include correct entry requirements, motivation to attend the workshop as well as gender and geographical balance. Priority is given to PhD scholars followed by other researchers. Due to the high volume of applications from Swedish academia, we currently do not accept international applicants.Tools for Reproducible Research
2021-11-15 to 2021-11-19 (5 days)
Online
More info
One of the key principles of proper scientific procedure is the act of repeating an experiment or analysis and being able to reach similar conclusions. Published research based on computational analysis, e.g. bioinformatics or computational biology, have often suffered from incomplete method descriptions (e.g. list of used software versions); unavailable raw data; and incomplete, undocumented and/or unavailable code. This essentially prevents any possibility of attempting to reproduce the results of such studies. The term “reproducible research” has been used to describe the idea that a scientific publication based on computational analysis should be distributed along with all the raw data and metadata used in the study, all the code and/or computational notebooks needed to produce results from the raw data, and the computational environment or a complete description thereof. Reproducible research not only leads to proper scientific conduct but also provides other researchers the access to build upon previous work. Most importantly, the person setting up a reproducible research project will quickly realize the immediate personal benefits: an organized and structured way of working. The person that most often has to reproduce your own analysis is your future self!RNAseq data analysis
2021-11-15 to 2021-11-19 (5 days)
Online
More info
This workshop will introduce the best practice bioinformatics methods for processing and analyses of RNA-seq data via a series of lectures and computer practicals.This workshop will introduce the best practice bioinformatics methods for processing and analyses of RNA-seq data via a series of online lectures and computer practicals. **Audience** National workshop open for PhD students, postdocs, researchers and other employees within Swedish academia. This course is run by the National Bioinformatics Infrastructure Sweden (NBIS). **Fee** 1800 SEK (for academic participants, please contact us for more information on the non-academic fee). Please note that NBIS cannot invoice individuals. The fee covers lunches, coffee and a course dinner. Those who accept the spot and then do not attend without prior notification will also be invoiced. **Note that travel and accommodation is not included in the fee and must be arranged by the participants. ** **Precourse material** Please read carefully the [Pre-course instructions](https://uppsala.instructure.com/courses/77082/pages/pre-course-instructions) material before the course start. If you have any problems with pre-course installations, please ask your questions in [Installation and pre-course related issues](https://uppsala.instructure.com/courses/77082/discussion_topics/238629). **Youtube videos** [RNASeq workshop videos](https://www.youtube.com/watch?v=VKhByCYa1R0&list=PLBsJUKzoJTHSGFT1f3WkU7tojmSLPvWVW)Epigenomics Data Analysis: from Bulk to Single Cell
2021-10-25 to 2021-10-29 (5 days)
Online
More info
The aim of this workshop is to introduce best practice bioinformatics methods for processing, analyses and integration of epigenomics data. The online teaching includes lectures, programming tutorials and interactive group sessions. This workshop is run by the National Bioinformatics Infrastructure Sweden (NBIS). **Audience** Course open to PhD students, postdocs, and other researchers. Note that priority is given to Swedish academia. **Fee** This online training event has no fee. However, if you confirm your participation but do not do so (no-show) you will be invoiced 2000 SEK. Please note that NBIS cannot invoice individuals. By accepting to participate in the course, you will be agreeing to follow the [NBIS Training Code of Conduct](https://uppsala.instructure.com/courses/48087/pages/nbis-training-code-of-conduct). We will issue a course certificate upon a successful course completion, assessed by active participation in all course sessions (lectures, computer practicals, group discussion etc.). Unfortunately we are **not** able to warrant any university credits (högskolepoäng). Many universities however, recognize the attendance in our courses and award 1.5 HPs, corresponding to a 40 h of studying. It is up to participants to clarify and arrange credit transfer with the relevant university department.Python programming with applications to bioinformatics
2021-10-18 to 2021-10-22 (5 days)
Online
More info
This course provides a practical introduction to the writing of [Python](https://www.python.org/) programs for the complete novice. Participants are lead through the core aspects of Python illustrated by a series of example programs. Upon completion of the course, attentive participants will be able to write simple Python programs from scratch and to customize more complex code to fit their needs. - The course is suitable for complete beginners and assumes no prior programming experience (beyond the ability to use a text editor). - A very basic knowledge of UNIX would be an advantage, such as navigating through folders and issuing commands at a shell prompt. We will not teach Unix in detail: Other course are available at SciLifeLab for it. Before the first lecture, we require you to follow the steps detailed in the [pre-course material](https://uppsala.instructure.com/courses/85913/pages/pre-course-material). **Audience** Course open to PhD students, postdocs, and other researchers. Note that priority is given to Swedish academia. **Fee** A course fee of 3000 SEK will be invoiced to accepted participants. This includes lunches, coffee and snacks, and course dinner. Please note that NBIS cannot invoice individuals By participating you will be agreeing to the [NBIS Code of Conduct](https://uppsala.instructure.com/courses/85913/pages/nbis-training-code-of-conduct?module_item_id=836091).Introduction to Data Management Practices
2021-10-12 to 2021-10-14 (3 days)
Online
More info
This course will introduce important aspects of Research Data Management through a series of lectures and hands-on computer exercises. The course is intended for researchers that want to take the first steps towards a more systematic and reproducible approach to analysing and managing research data. **Application instructions** National course open for PhD students, postdocs, researchers and other employees within all Swedish universities. The course is geared towards life scientists wanting to take the first steps towards a more systematic and reproducible approach to analysing and managing research data. **Fee** We charge a fee for onsite course occasions, to be paid by invoice to NBIS. This includes lunches, coffee and snacks. _Please note that NBIS **cannot** invoice individuals._Introduction to Biostatistics and Machine Learning
2021-10-04 to 2021-10-08 (5 days)
Online
More info
National course open for PhD students, postdocs, researchers and other employees in need of biostatistical skills within all Swedish universities. The course is geared towards life scientists wanting to be able to understand and use basic statistical and machine learning methods. It would also suit those already applying biostatistical methods but have never got a chance to truly understand the basic statistical concepts, such as the commonly misinterpreted p-value. **Fees** 2000 SEK includes lunches and coffee **Travel info** For travel information and hotel bookings see Travel Information page **Course credits** - Upon successful course completion, assessed based on active participation in all course session, we will issue a course certificate. - Please note that we are not able to provide any formal university credits (högskolepoäng). Many universities, however, recognize the attendance in our courses, and award 1.5 HPs, corresponding to 40h of studying. It is up to participants to clarify and arrange credit transfer with the relevant university department. **Selection criteria** - Due to limited space the course can accommodate maximum of 25 participants. If we receive more applications, participants will be selected based on several criteria. Selection criteria include correct entry requirements, motivation to attend the course as well as gender and geographical balance. - NBIS prioritises academic participants (students, staff, affiliated researchers) in Sweden. We can accept participants from industry and/or outside Sweden if we have seats available and the requirements criteria are met.Snakemake BYOC (bring-your-own-code) workshop
2021-09-29 to 2021-10-01 (3 days)
Online
More info
As data analysis projects grow and change over time, it gets increasingly difficult to keep track of how the different parts of the data analysis fit together. Workflow management systems such as Snakemake Links to an external site. can be used to set up, perform and monitor defined sequences of computational tasks ("workflows"), thereby making data analyses reproducible and scalable. Snakemake was developed in the bioinformatics community and has some features that make it particularly well-suited for bioinformatic workflows. The NBIS Tools for reproducible research course is held twice a year and provides both an introduction to Snakemake and a tutorial on how to use it. This Snakemake BYOC (bring-your-own-code) workshop provides a follow-up to that introduction. Here, participants will get support from experienced bioinformaticians to A) convert their data analysis from a programming language such as Bash, R or Python into a Snakemake workflow, OR B) apply more advanced techniques to their existing Snakemake workflows. **Audience** Workshop open for PhD students (prioritized), postdocs, researchers and others who have previously participated in the [NBIS Tools for reproducible research course](https://uppsala.instructure.com/courses/82575) or with demonstrated experience in writing Snakemake workflows. **Fee** This online training event has no fee. However, if you confirm your participation but do not do so (no-show) you will be invoiced 2,000 SEK. Please note that NBIS cannot invoice individuals. By accepting to participate in the workshop, you will be agreeing to follow the NBIS Training Code of Conduct. Due to limited space, the workshop can accommodate a maximum of 12 participants. If we receive more applications, participants will be selected based on several criteria. Selection criteria include correct entry requirements, motivation to attend the workshop as well as gender- and geographical balance. This is a national workshop. The workshop is open for PhD students, postdocs, group leaders and core facility staff. We do accept applications from other countries, but give priority to applicants from Swedish universities prior to applicants from industry and academics from other countries. Please note that NBIS training events do not provide any formal university credits. The training content is estimated to correspond to a certain number of credits; however, the estimated credits are just guidelines. If formal credits are crucial, the student needs to confer with their home department before submitting a workshop application in order to establish whether the workshop is valid for formal credits or not.BiG Talks – Metabolic Atlas: genome-scale metabolic models for easy browsing and analysis
BiG Talks – Network-based integration and visualization of large-scale data
BiG Talks – Network based analysis of 1002 GWAS study defines a pleiotropy map of human cell biology
Data visualization in R
2021-09-08 to 2021-09-09 (2 days)
Online
More info
This is a nation-wide course open for people who are interested in learning to plot using different packages in R. The course is organized by [NBIS](https://nbis.se/) (ELIXIR-SE). - This course aims to help researchers to visualize their data in different ways using R. This course will also aim to show researchers how they can make publication grade figures using R. - A part of this course is also about making interactive plots that the researchers can view and share in a web-server to make interactive visualizations of the data. **AUDIENCE** National course open for PhD students (prioritized), postdocs, researchers and other employees within all Swedish universities interested in learning to plot using different packages in R. **FEE** The fee for this on-site workshop is 2000 SEK to be paid by invoice to NBIS. Please note that NBIS cannot invoice individuals so we need your institutional invoicing address. The fee covers lunches, coffee and a course dinner. Those who accept the spot and then do not attend without prior notification will also be invoiced. Note that travel and accommodation is not included in the fee and must be arranged by the participants.Omics Integration and Systems Biology
2021-09-06 to 2021-09-10 (5 days)
Online
More info
**Application** Course open for PhD students, postdocs, group leaders and core facility staff from Sweden and European institutions looking for an introduction to multi-omics integration and systems biology approaches. Please note that NBIS training events do not provide any formal university credits. If formal credits are crucial, the student needs to confer with the home department before submitting a course application in order to establish whether the course is valid for formal credits or not. [Click here](https://forms.gle/Qet7uJnsJqQdtY2h7) if you would like to be notified of the next course instance. **Fee** This workshop has a fee of 3000kr and will be invoiced to the selected participants (Please note that NBIS cannot invoice individuals). Applications without complete invoice information will not be considered. Course fees cover all coffee breaks, all lunches and 1 course dinner.
