Education

Training Sessions

The BICF provides ongoing training through seminars and workshops hosted by our research faculty and core personnel. Individual bioinformatics software training is also available by request. Bioinformatics consulting will be provided through the help desk, available daily or through individual appointment requests (email Core Manager).

BICF/BioHPC Courses

BICF/BioHPC training sessions will take place each Wednesday at 10:30 a.m. in seminar room NL06.215, unless otherwise noted below. Visit the BioHPC portal for a full listing of dates and presenters.

Spring 2017 Training Sessions

1/4/2017

Introduction to BioHPC

 New User Training

1/11/2017

Using the SLURM Job Scheduler - Fundamentals of running computational jobs efficiently on the BioHPC cluster; Will cover serial and parallel jobs of various types

 General Computing Topics

1/18/2017

Linux Command Line Basics - Introduction to the Linux command line, basic tools and shell scripting

 Computer Science Topics

1/25/2017

User Showcase - Ranganathan group, web-based Psyca

 User Showcase

*NOTE: This training will be held in NL12.125.

2/1/2017

Introduction to BioHPC

 New User Training

*NOTE: This training will be held in NL12.125.

2/8/2017

Using BioHPC Thin Clients & Workstations - An introduction to the capabilities and usage of BioHPC thin-client and workstation machines

 General Computing Topics

2/15/2017

Keep Big Projects Under Control - High level discussion of strategies for software development, e.g., defensive programming, writing reusable/readable code, etc.

 Computer Science Topics

2/22/2017

User Showcase - astrocyte BICF workflow RNA-Seq analysis

 User Showcase

3/1/2017

Introduction to BioHPC

 New User Training

3/8/2017

BioHPC Cloud Storage & Backup - Fundamentals of BioHPC storage; How to access, transfer and share data using the web and other methods; Workflows for core facilities / data generating instruments; Detailed explanation of backup arrangements

 General Computing Topics

3/15/2017

Monitoring and Troubleshooting on BioHPC - Understanding the performance of your job; Introduce tools to help users monitor resource usage; General troubleshooting including software, Linux system, resource management, etc.

 Computer Science Topics

3/22/2017

User Showcase - BICF/QBRC lung and kidney cancer explorer

 User Showcase

3/29/2017

No training session

 

4/5/2017

Introduction to BioHPC

 New User Training

4/12/2017

Git on BioHPC - Introduction to basic Git version control workflows and the BioHPC Git service (Please note follow-up session on 7/19/2017.)

 General Computing Topics

4/19/2017

File Sharing Solutions - Introduce new BioHPC FTP and Cloud services (This session will be useful if you plan to attend the UCSC genome browser session on 9/27/2016.)

 Computer Science Topics

4/26/2017

Introduction to Proteomics Data Analysis on BioHPC - Introduction to the analysis of shotgun mass-spectrometry proteomics data, and to a number of tools available on BioHPC for proteomics projects; covers basic principles of peptide identification, protein inference, and quantitation.

 General Computing Topics

5/3/2017

Introduction to BioHPC

 New User Training

5/10/2017

Visualization on BioHPC - An overview of the visualization software and workflows available on the BioHPC cluster; convering visualization of extremely large data and integration into data analysis workflows

 General Computing Topics

5/17/2017

Parallel Programming in Matlab on BioHPC (MDCS and parallel tool box) - Speed up your Matlab analyses using parallel methods to execute code across the BioHPC cluster

 Computer Science Topics

5/24/2017

User Showcase - Danuser group

 User Showcase

5/31/2017

No training session

 

6/7/2017

Introduction to BioHPC

 New User Training

6/14/2017

Job Runner/Parameter Explorer - New platform release

 General Computing Topics

6/21/2017

Database System Design - From Excel to MySQL 

 Computer Science Topics

6/28/2017

User Showcaseastrocyte BICF workflow mutations analysis

 User Showcase

 

Fall 2017 Training Sessions

7/5/2017

Introduction to BioHPC

 New User Training

7/12/2017

Using the SLURM Job Scheduler - Fundamentals of running computational jobs efficiently on the BioHPC cluster; Will cover serial and parallel jobs of various types

 General Computing Topics

7/19/2017

Managing Software Projects in a Team - Expanding from the Git training, will cover how to structure a software project to work successfully in a team; Git workflow for team projects; How to track bugs and features; Good practices for testing and CI

 Computer Science Topics

7/26/2017

User Showcase - CRISPR sgRNA design and analysis

 User Showcase

8/2/2017

Introduction to BioHPC

 New User Training

8/9/2017

Using BioHPC Thin Clients & Workstations - An introduction to the capabilities and usage of BioHPC thin-client and workstation machines

 General Computing Topics

8/16/2017

How to use the UCSC Genome Browser and TCGA

 Computer Science Topics

8/23/2017

TBD Bioinformatics User Showcase

 User Showcase

8/30/2017

No training session

 

9/6/2017

Introduction to BioHPC

 New User Training

9/13/2017

BioHPC Cloud Storage & Backup - Fundamentals of BioHPC storage; How to access, transfer and share data using the web and other methods; Workflows for core facilities / data generating instruments; Detailed explanation of backup arrangements

 General Computing Topics

9/20/2017

Data Security & Management

 Computer Science Topics

9/27/2017

User Showcase - astrocyte GCRB/BICF workflows for Chip-Seq analysis

 User Showcase

10/4/2017

Introduction to BioHPC

 New User Training

10/11/2017

The BioHPC Nucleus Cluster - Will introduce advanced users to the structure of the BioHPC cluster; What is the significance of the way it is designed - IB network, types of storage etc.; Technical details for  users; Focus on how  design affects the best way to run jobs, etc. 

 General Computing Topics

10/18/2017

Parallel R/R on BioHPC

 Computer Science Topics

10/25/2017

TBD Bioinformatics User Showcase

 User Showcase

11/1/2017

Introduction to BioHPC

 New User Training

11/8/2017

Astrocyte workflow platform - new web based developer function release

 General Computing Topics

11/15/2017

Parallel Python

 Computer Science Topics

11/22/2017

No training session

 

11/29/2017

User Showcase - running microbiome analysis on the BioHPC

 User Showcase

12/6/2017

Introduction to BioHPC

 New User Training

12/13/2017

BioHPC NGS Web Toolkit - Introduction to the BioHPC NGS RNA-Seq Web toolkit; new version release

 General Computing Topics

12/20/2017

Next Generation BioHPC-HPC - Cloud On-Demand and DMZ HPC

 Computer Science Topics

12/27/2017

No training session