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Bioinformatics Show all

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)

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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.

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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 Show all

Data Analysis with R (January 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 two-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 and plotting.The course topics include data importing and exporting, handling real-life data sets and creating publication-ready plots with R. The topics will be covered using both hands-on teaching and independent exercises.

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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 Show all

New to command line? Test your skills!

To access and use supercomputers like Puhti and Mahti, you need to be able to work with text-based command line. This is a new challenge to many people more used to using graphical user interfaces like Windows and Mac OS. In many of our courses, we have "basic Linux skills" as a prerequisite. To help our course participants and users past this first barrier, we created this course. Before participating our courses with the basic Linux skills prerequisite, please go through this material and skill tests -this way you'll make sure you and other participants get the most out of the course!

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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

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Programming Languages Show all

Fortran Programming for Scientific Computing, Autumn 2020

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Introduction to Linux online

This course will go through the very basics of Linux/Unix utilization, mainly through the shell (text-based user interface). We do not expect any previous knowledge of the topic, just basic skills to operate any computer. No programming knowledge is expected. At the end of this course the student should survive in a complete shell-based Linux/Unix environment, like one finds when logging into large computing serves, such as those at CSC.Mainly driven by the current situation, this is a complete online course. It is split into a preparatory phase of one week where the students should read some basic background and install a virtual machine containing the Linux system we use during the course. The second week then will be a mixture of online studies and interactive work.

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Linux-2: Advanced command line use and Bash programming, study group autumn 2020

CSC training course for advanced command line use, common GNU/Unix tools, and Bash programming.To whom: You are already using Linux command line and writing Bash scripts, but would like to know better how do these actually work. After this course you should be able to use command line more efficiently, and write more elegant shell scripts, and fix the misbehaving ones.The course is organised as an intensive on-line study group. Short lecture type material and exercises contain questions that the students first study independently or in small groups, and are then discussed in the course forum and in on-line meetings.

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Introduction to LINUX

This two day course will cover the very basics of Unix/Linux. No previous knowledge about these operating systems is expected, as the course serves as an introduction to those who are completely new to Linux. Both days have extended hands-on exercises.The course will give the participant the basic knowledge and skills to use the Unix shell. How to navigate around, copy files and launch applications. In addition to being useful on CSC's servers, basic unix skills may come in handy elsewhere too, and knowing the basics makes later self study much easier. The hands-on exercises also will include a demonstration on how to set up one's own Linux system.

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DEMO Show all

H5P material bank

Location for sharing/embedding H5P material outside of e-Lena

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H5P and interactive tools

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