- VBCF courses - lists.vbcf.ac.at

[VBC-SCIENCE] CBE HPC cluster introduction course announcement
by Aszodi,Andras Oct. 2, 2025

Oct. 2, 2025

Dear Colleagues, I am pleased to announce the CBE HPC cluster introduction course which is highly recommended to all new users of the CBE cluster system. For details, see https://training.vbcf.ac.at/training/cbe.php . WHEN? Friday the 10th February from 09:00 to 13:00. WHERE? PHYSICALLY in the IMP seminar room E-016 (preferred option), and REMOTELY via teleconferencing. The latter option is ONLY for non-VBC employees and moderately sick colleagues. WHO MAY ATTEND? Anyone who may use the CBE system (IMP,IMBA,GMI,VBCF employees and external colleagues with cluster access). If you plan to use the cluster in the near future then you'll need a cluster account (see below). WHAT DOES IT COST? It's free of charge. PRE-REQUISITES: - You must have a CBE cluster account (our IT will set it up if needed). - VBC VPN access if you are at the UBB or a non-VBC institution (e.g. OeAW). - Basic UNIX command line experience. If you attended my command line course https://training.vbcf.ac.at/training/unix.php then you are well prepared. - Bash scripting experience is advantageous but not necessary. HOW TO REGISTER? Make sure your supervisor agrees, and then register yourself at https://training.vbcf.ac.at/training/schedule.php#curcrs . CONSULT YOUR CALENDAR, check if you have NO OTHER COMMITMENTS. Then click on the "Register" button and fill out the little online form. Please keep in mind that a confirmed registration involves a COMMITMENT TO ATTEND. Reason: There is quite some work involved in preparing your work environment and your hands-on exercises. Plus the number of participants is limited, don't take away a slot from a colleague. See additional details at https://training.vbcf.ac.at/training/practical_information.php Thanks a lot, András You are receiving this message because you are subscribed to the VBC Science mailing list. To unsubscribe from this list, go to here<https://myaccount.microsoft.com/groups/64dd6714-c5a4-4ec9-a794-e7d168bf2f88> and select "Leave". If you want to re-join at a later time, visit this link<https://myaccount.microsoft.com/groups/search> and search for "VBC List" groups to join.

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[VBC-SCIENCE] UNIX course announcement
by Aszodi,Andras Sept. 30, 2025

Sept. 30, 2025

Dear Colleagues, I am pleased to announce my UNIX command line course https://training.vbcf.ac.at/training/unix.php which is especially recommended to those who plan to use the campus HPC cluster. NOTE THAT THIS IS NOT THE CLUSTER COURSE, that will come on the 10th October. However, it also serves as the foundation for the Bash scripting course which will be offered later (planned for the 16th October). TOPICS: - UNIX overview: general principles. - Working with files and directories. - Users, groups, permissions, environment variables. - Command pipelines, job control. DATE/TIME: Tuesday the 7th October, 09:00 - 13:00. LOCATION: "Live" at the IMP seminar room E-016. Online participation is not offered since it's very difficult to correct typing mistakes "remotely". PREREQUISITES: This is a basic introduction to UNIX, only good typing skills are required. COST: Free of charge. HOW TO REGISTER: First of all: If you register and then don't attend, then you take away a place from a colleague. Please plan ahead responsibly. See also https://training.vbcf.ac.at/training/practical_information.php 1) Check your calendar! 2) Ask your PI. 3) Go to the Training schedule page https://training.vbcf.ac.at/training/schedule.php, click on the UNIX command line "Register" button and fill out the little form. Thanks, András VBCF Computational Biology Training Expertise Hub You are receiving this message because you are subscribed to the VBC Science mailing list. To unsubscribe from this list, go to here<https://myaccount.microsoft.com/groups/64dd6714-c5a4-4ec9-a794-e7d168bf2f88> and select "Leave". If you want to re-join at a later time, visit this link<https://myaccount.microsoft.com/groups/search> and search for "VBC List" groups to join.

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[VBC-SCIENCE] "Think statistics!" - course announcement
by Aszodi,Andras Sept. 12, 2025

Sept. 12, 2025

Dear Colleagues, I have the honour to announce my "Think statistics!" course (more info at https://training.vbcf.ac.at/training/rstat.php ) The main aim of this course is to teach you to how to approach data analysis problems with classical statistics. We will focus on the intuition behind statistical methodologies, rather than on mathematical details. TOPICS: - Sampling theory: obtaining information about a population via sampling. Sample characteristics (location, dispersion, skewness). - Central Limit Theorem and the Normal distribution. - The distribution of the sample mean. Confidence interval of the mean. - Basic principles of hypothesis testing. "Student"'s t-test. - Type I and Type II errors. P-value distributions. Power calculations. - "Cookbook of tests": distribution tests (Shapiro, Kolmogorov-Smirnov), parametric and non-parametric tests (e.g. Wilcoxon), counting statistics, contingency tables (chi-square test), correlation tests. OUT OF SCOPE: Bioinformatics data analyses. SCIENTIFIC PREREQUISITES: - Basic probability concepts. - Working with (continuous) probability distributions. PROGRAMMING PREREQUISITES: Basic familiarity with R is of advantage to understand the hands-on examples and to complete the homework assignments after Day 1. DATE/TIME: 22nd-23rd September (Monday-Tuesday), from 09:00 to 13:00 on both days. Please reserve some time in the afternoon for the voluntary homework assignment. LOCATION: IMP seminar room E-016. Remote attendance is offered to colleagues outside the VBC. COST: free of charge. HOW TO REGISTER: 1) Check your calendar. *** If you register but don't attend, you are taking away a place from a colleague! *** 2) Ask your supervisor for permission to attend. 3) Inform your supervisor that you won't be available during the course. (No last-minute forgotten lab meetings etc! :-) ) 4) Open this URL: https://training.vbcf.ac.at/training/schedule.php Click on the [REGISTER] button and fill out the form. Use an Austrian academic email address. Please specify your job type (e.g. “PhD student”) correctly. Thank you and have a nice weekend, András You are receiving this message because you are subscribed to the VBC Science mailing list. To unsubscribe from this list, go to here<https://myaccount.microsoft.com/groups/64dd6714-c5a4-4ec9-a794-e7d168bf2f88> and select "Leave". If you want to re-join at a later time, visit this link<https://myaccount.microsoft.com/groups/search> and search for "VBC List" groups to join.

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[VBC-SCIENCE] Probability theory course announcement
by Aszodi,Andras Sept. 5, 2025

Sept. 5, 2025

Trying to get ahead in science without speaking English? It won't work. Trying to get ahead in science without understanding probability theory? It won't work either. I am pleased to announce my "Probability Theory (with R)" course (more info at https://training.vbcf.ac.at/training/rprob.php ) . This course teaches you the basics of probability theory which is indispensable for any scientific investigation. We will focus on the intuition behind probability theory rather than on a mathematically rigorous presentation. This course is a pre-requisite to the "Think statistics! (with R)" course (https://training.vbcf.ac.at/training/rstat.php ). TOPICS: - Foundations of probability theory: basic identities (sum rule, product rule). Independent variates, conditional probability. - Discrete probability distributions: Uniform, Bernoulli, Binomial, Poisson, Negative Binomial. - Continuouos probability distributions: Uniform, Exponential, Gamma etc. - Central Limit Theorem. Normal and Chi-square distributions. OUT OF SCOPE: Applied data analyses as this is a foundational course. SCIENTIFIC PREREQUISITES: Knowledge of the 4 arithmetic operations. The rest I'll explain. PROGRAMMING PREREQUISITES: Basic familiarity with R is needed to understand the hands-on examples. DATE/TIME: Wednes the 17th September, 09:00 - 13:00h. LOCATION: IMP seminar room E-016. COST: free of charge. HOW TO REGISTER: Check your calendar. *** If you register but don't attend, you are taking away a place from a colleague! ***. Ask your supervisor for permission to attend, then open this URL: https://training.vbcf.ac.at/training/schedule.php Click on the [REGISTER] button and fill out the form. Please specify your job type (e.g. “PhD student”) correctly. Thank you, András You are receiving this message because you are subscribed to the VBC Science mailing list. To unsubscribe from this list, go to here<https://myaccount.microsoft.com/groups/64dd6714-c5a4-4ec9-a794-e7d168bf2f88> and select "Leave". If you want to re-join at a later time, visit this link<https://myaccount.microsoft.com/groups/search> and search for "VBC List" groups to join.

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[VBC-SCIENCE] R programming course announcement
by Aszodi,Andras Sept. 2, 2025

Sept. 2, 2025

Dear Colleagues, I am pleased to announce my "R as a Programming Language" course (more info at https://training.vbcf.ac.at/training/rlang.php ). This introductory course serves as the foundation for my biostatistics trainings and teaches you the basics of the R programming language. Please read the following information carefully until the end. Who may attend? If you have received this email, you may sign up :-) However, preference is given to the "new" PhD students as discussed during the "Prime Your PhD" boot camp. Topics: • Introduction to R: general principles. • Data structures in R: vectors, matrices, arrays, lists, data frames. Data import/export. • Functions in R: how to write your own functions and scripts. • Visualization in R: various plot types ("classic" built-in graphics only). Out of scope: We won't discuss statistics at all. Basic biostatistics and more advanced data analysis/machine learning courses will come soon. Prerequisites: Typing skills. Experience with other programming languages is advantageous but not needed. Date/Time: 10th and 11th September (Wed-Thu), 09:00 - 13:00 on both days. Attendance: physical only, no remote participation. Reason: it's very difficult to correct typos over Zoom. Cost: free of charge. How to register: 1) Check your calendar. *** If you register but don't attend, you are taking away a place from a colleague! *** 2) Ask your supervisor for permission to attend. 3) Inform your supervisor that you won't be available during the course. (No last-minute lab meeting presentations etc!) 4) Open this URL: https://training.vbcf.ac.at/training/schedule.php Click on the [REGISTER] button and fill out the form. Please specify your job type correctly. Thank you, András You are receiving this message because you are subscribed to the VBC Science mailing list. To unsubscribe from this list, go to here<https://myaccount.microsoft.com/groups/64dd6714-c5a4-4ec9-a794-e7d168bf2f88> and select "Leave". If you want to re-join at a later time, visit this link<https://myaccount.microsoft.com/groups/search> and search for "VBC List" groups to join.

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[VBC-SCIENCE] Clustering and Classification with Python course announcement
by Aszodi,Andras Aug. 26, 2025

Aug. 26, 2025

Dear Colleagues, I have the pleasure to announce the world premiere of my "Clustering and Classification with Python" course, part of my "machine learning"/"advanced statistical modelling" collection. The course provides a short introduction to the huge subject of clustering and classifying observations. For more details visit https://training.vbcf.ac.at/training/pyclassif.php . Topics: * Hierarchical clustering, k-means clustering. * Gaussian mixtures, E-M algorithm. * Quadratic and linear discriminant analysis. * Feature selection with principal components. * Cross-validation techniques. * Logistic regression and its connection with discriminant analysis. Multinomial regression. When? Friday 5th September, 09:00 - 13:00. Where? IMP seminar room E-016. Pre-requisites: You must know Python, and be familiar with NumPy and Pandas. Cost: Free of charge. How to register? Make sure you don't have any meetings on that date, ask your boss for permission to attend, and then sign up at https://training.vbcf.ac.at/training/schedule.php by filling out the little form. Sign up only if you are confident that you will attend, don't take away a slot from a colleague. Keep in mind the general attendance rules, see https://training.vbcf.ac.at/training/practical_information.php for details. You will get a confirmation from me later this week. Thank you, András You are receiving this message because you are subscribed to the VBC Science mailing list. To unsubscribe from this list, go to here<https://myaccount.microsoft.com/groups/64dd6714-c5a4-4ec9-a794-e7d168bf2f88> and select "Leave". If you want to re-join at a later time, visit this link<https://myaccount.microsoft.com/groups/search> and search for "VBC List" groups to join.

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[VBC-SCIENCE] Python programming course announcement (LONG!)
by Aszodi,Andras Aug. 5, 2025

Aug. 5, 2025

Dear Colleagues, I have the pleasure to announce my "Python programming" course (see https://training.vbcf.ac.at/training/pylang.php ) Please read the following information CAREFULLY TO THE END TO AVOID DISAPPOINTMENT. COURSE DIFFICULTY: This is an "entry-level" course that starts from the very basics of Python programming. However, towards the end we will move to more complex concepts. Please DO READ the "TOPICS" section below carefully! DATES/TIMES: The course consists of two parts, and both parts involve two four-hour sessions (16 hours in total). You must take both Part I and Part II because they build on each other. PART I: 25th and 26th August (Monday-Tuesday), 09:00 - 13:00 PART II: 27th and 28th August (Wednesday-Thursday), 09:00 - 13:00 Reserve day: Friday the 29th August 09:00 - 13:00 if we need some extra time. PLEASE DO CHECK YOUR CALENDAR BEFORE SIGNING UP! Make sure you can attend ALL sessions (i.e. all mornings on the week 25-29 Aug). Do not take away slots from others by signing up and then not joining. EXERCISES: There will be "homework" assignments after Days 1,2,3 so plan about 1-2 hours for them in the afternoons/evenings to work on them at your own pace. TOPICS: Day 1: - Introduction to Python: basic principles. - Python data structures: strings, tuples, lists, dictionaries, sets. Day 2: - Object-oriented programming in Python. Encapsulation, inheritance (base and derived classes), polymorphism. Day 3: - Writing a Python class using test-driven development techniques. Day 4: - Writing Python scripts. Command-line option processing, file I/O, error handling. OUT OF SCOPE: - No data analysis! This course is only about the Python language itself. - No personal projects! We will work on a simple task (genomic region manipulation) together. I don't have the resources to supervise individual projects of the participants. PREREQUISITES: - You must be able to type quickly with a low error rate, otherwise you'll hold up everybody else. - Previous experience with another programming language is highly desirable but not mandatory. VENUE: Seminar room 1.2 at the UBB. Physical attendance only. COST: Free of charge. NUMBER OF PARTICIPANTS: Strictly limited to 18. First come, first served. Please sign up only if you can attend all four sessions! HOW TO REGISTER: Ask your supervisor for permission to attend, then open this URL: https://training.vbcf.ac.at/training/schedule.php . Click on the [REGISTER] button of Part I of the course, this will register you to Part II as well. (It is not possible to register for only one part.) Then fill out the registration form. Please specify your job type correctly. Use an Austrian academic email address. You will get an automated acknowledgement mail, and in a few days a final confirmation from me. After that, PARTICIPATION BECOMES MANDATORY. Please consult https://training.vbcf.ac.at/training/practical_information.php for details. Thank you, András You are receiving this message because you are subscribed to the VBC Science mailing list. To unsubscribe from this list, go to here<https://myaccount.microsoft.com/groups/64dd6714-c5a4-4ec9-a794-e7d168bf2f88> and select "Leave". If you want to re-join at a later time, visit this link<https://myaccount.microsoft.com/groups/search> and search for "VBC List" groups to join.

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[VBC-SCIENCE] CBE HPC intro course announcement
by Aszodi,Andras June 6, 2025

June 6, 2025

Dear Colleagues, I am pleased to announce the CBE HPC cluster introduction course which is highly recommended to all new users of the CBE cluster system. For details, see https://training.vbcf.ac.at/training/cbe.php . WHEN? Monday the 16th June from 09:00 to 13:00. WHERE? PHYSICALLY in the IMP seminar room E-016 (preferred option), and REMOTELY via teleconferencing. The latter option is ONLY for non-VBC employees and moderately sick colleagues. WHO MAY ATTEND? Anyone who may use the CBE system (IMP,IMBA,GMI,VBCF employees and external colleagues with cluster access). If you plan to use the cluster in the near future then you'll need a cluster account (see below). WHAT DOES IT COST? It's free of charge. PRE-REQUISITES: - You must have a CBE cluster account (our IT will set it up if needed). - VBC VPN access if you are at the UBB or a non-VBC institution (e.g. OeAW). - Basic UNIX command line experience. If you attended my command line course https://training.vbcf.ac.at/training/unix.php then you are well prepared. - Bash scripting experience is advantageous but not necessary. HOW TO REGISTER? Make sure your supervisor agrees, and then register yourself at https://training.vbcf.ac.at/training/schedule.php#curcrs . CONSULT YOUR CALENDAR, check if you have NO OTHER COMMITMENTS. Then click on the "Register" button and fill out the little online form. Please keep in mind that a confirmed registration involves a COMMITMENT TO ATTEND. Reason: There is quite some work involved in preparing your work environment and your hands-on exercises. Plus the number of participants is limited, don't take away a slot from a colleague. See additional details at https://training.vbcf.ac.at/training/practical_information.php Thanks a lot, András VBCF Computational Biology Training Expertise Hub You are receiving this message because you are subscribed to the VBC Science mailing list. To unsubscribe from this list, go to here<https://myaccount.microsoft.com/groups/64dd6714-c5a4-4ec9-a794-e7d168bf2f88> and select "Leave". If you want to re-join at a later time, visit this link<https://myaccount.microsoft.com/groups/search> and search for "VBC List" groups to join.

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[VBC-SCIENCE] Bayesian statistics course announcement
by Aszodi,Andras May 22, 2025

May 22, 2025

Dear Colleagues, I am pleased to announce my "Bayesian statistics (with R)" course (more info at https://training.vbcf.ac.at/training/rbayes.php ). The course will teach you the foundations and some specific applications of Bayesian methodologies. TOPICS: - Diagnostic kits: calculating the probability of being sick if you tested positive, using Bayes' Theorem. - Life and death of a mouse: Estimating the probability parameter of the Binomial distribution. Conjugate priors, updating the posterior. - Blood groups: from phenotype to genotype. Modelling hidden variables the Bayesian way. - Towards modelling causality: Introduction to Bayesian Networks. OUT OF SCOPE: As usual, we cannot address specific data analysis problems relevant to your projects. PREREQUISITES: You must have a solid grasp on how to calculate probabilities and be familiar with discrete and continuous distributions. If you attended my "Probability theory" course ( https://training.vbcf.ac.at/training/rprob.php ) then you are well equipped. Familiarity with the R programming language is not a requirement (but helpful for the exercises). DATE/TIME: Tuesday the 3rd June from 09:00 - 13:00. LOCATION: IMP seminar room E-016. Remote participation is offered to non-VBC colleagues only. EXERCISES: You will have the opportunity to practise what you learned using my online exercise setup. Ideally you should reserve about an hour in the afternoon following the lecture for this activity. COST: free of charge. HOW TO REGISTER: 1) Check your calendar. *** If you register but don't attend, you are taking away a place from a colleague! *** 2) Ask your supervisor for permission to attend. 3) Inform your supervisor that you won't be available during the course. (No last-minute forgotten lab meetings etc! :-) ) 4) Open this URL: https://training.vbcf.ac.at/training/schedule.php Click on the [REGISTER] button and fill out the form. Please specify your job type correctly. Thank you, András You are receiving this message because you are subscribed to the VBC Science mailing list. To unsubscribe from this list, go to here<https://myaccount.microsoft.com/groups/64dd6714-c5a4-4ec9-a794-e7d168bf2f88> and select "Leave". If you want to re-join at a later time, visit this link<https://myaccount.microsoft.com/groups/search> and search for "VBC List" groups to join.

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subscribe
by Resch, Stefan April 30, 2025

April 30, 2025

Stefan Resch Software Architect and NLP Analyst<https://github.com/SteffRhes> <https://www.oeaw.ac.at/acdh/team/current-team/stefan-resch>https://www.oeaw.ac.at/acdh/team/current-team/stefan-resch <https://github.com/SteffRhes>https://github.com/SteffRhes Austrian Centre for Digital Humanities & Cultural Heritage Austrian Academy of Sciences Bäckerstraße 13, 1010 Vienna, Austria

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