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Bioinformatics Näytä kaikki

BioMonth 2022
BioMonth 2022
In March-April 2022 we offer you a nice opportunity to learning how to use supercomputer Puhti to do your data processing or simulations effectively, and how to handle your data not only while doing the analysis, but also before and after that! Join the BioMonth 2022 classes and make sure you get the most out of our services* and your data management in shape!* The CSC services discussed in this course are free-of-charge for academic research, education and training purposes in Finnish higher education institutions and in state research institutes (subsidized by the Ministry of Education and Culture, Finland).  With 1 registration you get 3 half-days (9:00-12:00) of interesting topics:Wed 30.3. - Fri 1.4.Using CSC services efficiently from biousers point-of-viewSDS servicesData managementNote also:23.3.-25.3. Using CSC environment efficiently Wed 6.4.- Fri 8.4. RNA-seq data analysis with Chipster -separate registration!
Jatka kurssille
Containers and Workflows in Bioinformatics
Containers and Workflows in Bioinformatics
Bioinformatics tools often require installing different dependencies in a controlled environment. Containers allow you to logically package your application (e.g., a bioinformatics tool) together with libraries and other dependencies, providing isolated environments for running your software services. Containerised applications can be run in an isolated runtime environment independent of the actual environment (e.g., private data center, the public cloud, or even a developer’s personal laptop) in which the applications are running in. These are recently gaining popularity as a standard way to distribute, deploy, and run services by developers and system administrators. This course will focus on the deployment of containerised applications in HPC environment. The course will also introduce a modern workflows manager (i.e., nextflow ) to perform complex analysis in bioinformatics..
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BioMonth: CSC supercomputing and data management for bioscientists
BioMonth: CSC supercomputing and data management for bioscientists
In March you can spend your Tuesday and Wednesday mornings learning how to use supercomputer Puhti to do your data processing or simulations effectively, and how to handle your data not only while doing the analysis, but also before and after that! Join the BioMonth 2021 classes and make sure you get the most out of our services* and your data management in shape!* The CSC services discussed in this course are free-of-charge for academic research, education and training purposes in Finnish higher education institutions and in state research institutes (subsidized by the Ministry of Education and Culture, Finland).  With 1 registration you get 6 half-days (9:00-12:00) of interesting topics in March 2021.16.3. and 17.3.23.3. and 24.3.30.3. and 31.3.Description:Puhti is a CSC's supercomputer that comprises powerful CPU partitions with a wide range of memory sizes and local storage options. Puhti allows the user to reserve compute and memory resources flexibly, and the user can run anything from interactive single core data processing to medium scale simulations spanning multiple nodes. Puhti has a wide selection of scientific software installed.Allas is CSC's general-purpose research data storage server. It is a part of the CSC storage portfolio and can be accessed on the CSC servers as well as from anywhere on the internet. Allas can be used both for static research data that needs to be available for analysis and to collect and host cumulating or changing data.Good research data management is the basis of successful research. Research data management (RDM) concerns the managing and organisation of data during as well as after the active phase of a project. It is important to consider all stages of data management from collecting and processing the data to publishing and sharing it using a Data Management Plan (DMP). This will increase the impact and visibility of your work and enable reuse of the data in the future.Later this course we will introduce HPC-compliant containers called Singularity containers which allows Puhti users to run their applications in a containerised environment. These containers can serve as an alternative approach to conda packages.Puhti (16.-17.3. 9:00-12:00 EET (UTC+2))Getting started with PuhtiModule systemData storage in PuhtiRunning sbatch jobsPerformance analysisRunning interactive jobs in PuhtiData (23.-24.3. 9:00-12:00 EET (UTC+2))What is Allas? Projects, clients and interfaces.Examples for storing, using and sharing small or large datasets.Examples for using Allas from Puhti and from your local environmentResearch data management: what happens before and after computing?Data management planningSensitive data services offered by CSCPublishing and sharing data after the projectContainers (30.-31.3. 9:00-12:00 EET (UTC+2)) Introduction to SingularityRunning applications as singularity containersBuilding singularity containersConverting conda packages as singularity applicationsWorkflows with singularity containers (if this part is two days)
Jatka kurssille
Biocontainers (101):Containerised Applications in Bioinformatics
Biocontainers (101):Containerised Applications in Bioinformatics
This is a basic level course on containers which are a modern way of deploying complex applications. In this course, the basics of docker container and its containnerised applications in bioinformatics will be discussed. Emphasis will be given to the deployment of different pre-existing dockerised bio-applications. Selected examples from different omics’ disciplines such as genomics, proteomics and metabolomics will be covered. We will introduce HPC-compliant containers in CSC environment.
Jatka kurssille
Single cell RNA-seq data analysis with Chipster
Single cell RNA-seq data analysis with Chipster
This introductory course covers single cell RNA-seq data analysis methods, tools and file formats. The free* and user-friendly Chipster software is used in the exercises, and the course is thus suitable for everybody.* See: https://chipster.csc.fi/access.shtml
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Data Analytics Näytä kaikki

KLTO-132 (Statistics with R)
KLTO-132 (Statistics with R)
R is a language that has become one of the most popular tools for manipulating, visualizing and analyzing data. While there are many R courses, learning these skills can involve a steep learning curve, especially for people with no experience in programming or data analysis. This three-day remote course (delivered via Zoom) aims to help with this initial difficulty by equipping learners with essential skills in using R, including data wrangling, plotting and an introduction to statistical testing.The course topics include data importing and exporting, handling real-life data sets, creating publication-ready plots, and using selected statistical tests (t-test, linear regression, Chi-squared test) in R. The topics will be covered using hands-on teaching and independent exercises.
Jatka kurssille
Data Analysis with R (Nov 2021)
Data Analysis with R (Nov 2021)
R is a language that has become one of the most popular tools for manipulating, visualizing and analyzing data. While there are many R courses, learning these skills can involve a steep learning curve, especially for people with no experience in programming or data analysis. This three-day remote course (delivered via Zoom) aims to help with this initial difficulty by equipping learners with essential skills in using R, including data wrangling, plotting and statistics.The course topics include data importing and exporting, handling real-life data sets, creating publication-ready plots, as well as basic concepts of statistical testing with R. The topics will be covered using both hands-on teaching and independent exercises.
Jatka kurssille
Practical machine learning
Practical machine learning
An online course with 10 lectures offering a practical introduction to machine learning, including classification, regression, dimensionality reduction and unsupervised learning. Topics covered include linear classification and regression, nearest neighbor methods, support vector machines, decision trees, neural networks, clustering, and anomaly detection.
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HPC Näytä kaikki

CSC Puhti + R/RStudio Workshop
CSC Puhti + R/RStudio Workshop
This course is tailored for users who have previous experience with R and want to get started using R in CSC supercomputers.
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CSC Computing Environment
CSC Computing Environment
"This is what everyone should know about our HPC environment when launching jobs!"
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CSC Prerequisite minicourse
CSC Prerequisite minicourse
To access and use supercomputers like Puhti and Mahti, you need to be able to work with text-based Command Line Interface (CLI). This is a new challenge to many people who are more used to using Graphical User Interfaces (GUI) in Windows and macOS. This course provides users with "basic command line skills" that are a prerequisite in many CSC courses. To make sure you get the most out of the other courses, please go through this material and skill tests first. Happy journey on the command line!
Jatka kurssille
Using CSC HPC environment efficiently – Autumn 2021
Using CSC HPC environment efficiently – Autumn 2021
Jatka kurssille
Basic Command Line skills
Basic Command Line skills
To access and use supercomputers like Puhti and Mahti, you need to be able to work with text-based Command Line Interface (CLI). This is a new challenge to many people who are more used to using Graphical User Interfaces (GUI) in Windows and macOS. This course provides users with "basic command line skills" that are a prerequisite in many CSC courses. To make sure you get the most out of the other courses, please go through this material and skill tests first. Happy journey on the command line!
Jatka kurssille
Introduction to Parallel Programming
Introduction to Parallel Programming
The course introduces the basics of parallel programming with the message-passing interface (MPI) and OpenMP paradigms. MPI is the dominant parallelization paradigm in high performance computing and enables one to write programs that run on distributed memory machines, such as Puhti and Taito. OpenMP is a threading based approach which enables one to parallelize a program over a single shared memory machine, such as a single node in Puhti. The course consists of lectures and hands-on exercises on parallel programming. Course will be given in the online form, lectures are given in the mornings (third day is exception with lectures also in the afternoon), and after that the participants can work on hands-on exercise on their own pace. During the self-study sessions a chat room will be provided for peer-to-peer learning and for assistance from lecturers. Learning outcome After the course the participants should be able to write simple parallel programs and parallelize existing programs with basic features of MPI or OpenMP. This course is also a prerequisite for the PTC course "Advanced Parallel Programming" in 2021. Prerequisites and content level The participants are assumed to have a working knowledge of Fortran and/or C programming languages. In addition, fluent operation in a Linux/Unix environment will be assumed. The content level of the course is broken down as: beginner's - 60%, intermediate - 40%, advanced - 0%, community-targeted content - 0%.
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Using CSC HPC environment efficiently
Using CSC HPC environment efficiently
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