Slides & Handouts

Slides and handouts for past training sessions will be posted here.

 


Wednesday Mar 21st 2018 - Parallel Programming in MATLAB on BioHPC

Icon 20180321_Matlab_BioHPC.pdf (3.4 MB)

Icon matlab_demo.zip (2.6 MB)

 


Wednesday Mar 14th 2018 - Monitoring and troubleshooting on BioHPC

Icon 20180314_Monitoring_Troubleshooting.pdf (2.1 MB)

Icon inefficient_efficient_readers.tar.gz (2.3 KB)


Wednesday Mar 7th 2018 - Introduction of BioHPC

Icon 2018_03_07_BioHPC_Introduction.pdf (3.1 MB)

Icon hello_user.py (187 bytes)


Wednesday Feb 28st 2018 - Pathway Analysis

Icon PathwayAnalysis.pdf (8.1 MB)


Wednesday Feb 21st 2018 - Git Version Control

Icon Git-version_control.pdf (1.8 MB)

Icon demo-playbook.pdf (716.5 KB)


Wednesday Feb 7th 2018 - Introduction of BioHPC

Icon 2018_02_07_BioHPC_Introduction.pdf (3.4 MB)

Icon hello_user.py (187 bytes)


Wednesday Jan 24th 2018 - USCS Genome Browser & WashU Epigenome Browser

Icon 2018_01_24_UCSC_Genome_Browser_tutorial.pdf (16.4 MB)


Wednesday Jan 17th 2018 - Introduction to Web Based Machine Learning with DIGITS

Icon 20180117_DIGITS.pdf (1.9 MB)


Wednesday Jan. 10th 2018 - linux command line basics

Icon Linux Cli and basic shell scripting (1.5 MB)

Icon sample_scripts_zip (3.1 KB)


Wednesday 29th November 2017 - Point and Click 16S rRNASeq Analysis for Microbiome Studies

Icon Astrocyte16SrRNA.pdf (1.5 MB)

 


Wednesday 18th Oct 2017 - Parallel R / R on BioHPC

Icon 2017_10_18_R_On_BioHPC.pdf (2.2 MB)

Icon 2017_10_18_R_examples.zip (2.1 MB)


Wednesday 11th Oct 2017 - The BioHPC Nucleus Cluster & Future Developments

Icon 20171011_Nucleus_cluster.pdf (2.8 MB)


Wednesday 27th Sep 2017 - Astrocyte BICF workflow mutation analysis

Icon Astrocyte Variant Analysis and Visualization (5.2 MB)


Wednesday 20th Sep 2017 - Data Security & Management

Icon 2017_09_20_Security.pdf (1.9 MB)


Wednesday 16th Aug 2017 - UCSC Genome Browser Tutorial

Icon UCSC Genome Browser tutorial.pdf (11.2 MB)


Wednesday 2nd Aug 2017 - Introduction to BioHPC

Icon BioHPC_INTRO-8-02-17 (17.4 MB)


Wednesday 26th July 2017 - Astrocyte GCRB/BICF Workflow for ChIP-Seq Analysis

Icon Astrocyte GCRB/BICF Workflow for ChIP-Seq Analysis (6.3 MB)


Wednesday 19th July 2017 - Managing Software Project in a Team

Icon 2017_07_19_Managing_Software_Projects_Team.pdf (1.6 MB)


Wednesday 12th July 2017- Slurm Job Scheduler

Icon 2017_07_12_SLURM_JOB_Scheduler.pdf (2.0 MB)

Icon slurm_demo.zip (7.0 MB)


Wendesday 5th July 2017 - BioHPC New User Training

Icon 20170705_Intro (3.2 MB) Icon demo script (188 bytes)


Wednesday 28th Jun - Downstream Omics Analysis: Pathways, Heatmaps and Public Data

Icon bc_biohpc_downstreamOmics.pptx.pdf (3.0 MB)


Wednesday 21st Jun 2017 - Database System Design, From Excel to MySQL

Icon BICF_Training_20170621.pdf (3.5 MB)


Wednesday 14th Jun 2017 - BioHPC Parameter Runner

Icon 20170614_parameter_runner (2.1 MB)


Wendesday 7th Jun 2017 - BioHPC New User Training

Icon Training Slides (17.4 MB)


Wendesday 17th May 2017 - Parallel Programming in Matlab on BioHPC

Icon 20170517_Matlab_Parallel_Programming_BioHPC.pdf (3.0 MB)

Icon matlab_demo.zip (2.6 MB)


Wendesday 10th May 2017 - BioHPC Visualization

Icon 2017_05_10_BioHPC_Visualization.pdf (3.0 MB)

Icon visualization_demo_2017.zip (3.2 KB)


Wendesday 3rd May 2017 - Introduction to BioHPC

Icon 2017_05_03_BioHPC_Introduction.pdf (3.3 MB)


Wendesday 26th April 2017 - Introduction to Proteomics Data Analaysis. Tools & Techniques on BioHPC

Icon 2017_04_26_Proteomics_R1.pdf (2.5 MB)


Wednesday 19th April 2017 - File Sharing Solutions

Icon BioHPC-File Sharing Solutions (1.6 MB)


Wednesday 12th April 2017 - Git Version Control

Icon 20170412_git_version_control.pdf (1.7 MB)

Icon demo_playbook.pdf (716.5 KB)


Wednesday 5th April 2017 - Introduction to BioHPC

Icon 040517_intro_slides.pdf (1.5 MB)

Icon hello_user.py (187 bytes)


Wednesday 22nd March 2017 -  User showcase: Lung and kidney cancer explorer: Web-based integrative analysis of genomic and clinical data

Icon 2017_03_22_Lung_and_Kidney_Cancer_Explorers.pdf (2.0 MB)

 


Wednesday 15th March 2017 -  Monitoring and Trouble shooting

Icon 2017_03_15_Monitoring_Trouble_Shooting (1.8 MB)

 


Wednesday 1st March 2017 - New User Training

Icon 2017_03_01_BioHPC_Introduction.pdf (3.3 MB)

Icon verycomplicatedscript.py (188 bytes)

 


Wednesday 22nd February 2017-  User Showcase: Astrocyte RNASeq Analysis

Icon 2017_02_22_User_ Showcase_Astrocyte_RNASeq_Analysis_XL.pdf (3.1 MB)


Wednesday 15th February 2017-  Keeping Big Projects Under Control

Icon 2017_02_15_Big_Projects.pdf (1.9 MB)

Icon guide-conda_02-09.pdf (676.6 KB)


Wednesday 8th February 2017-  BioHPC Workstations and Thin Clients

Icon 2017-02-08_BioHPC_Workstations_and_Thin_Clients (1.6 MB)


Wednesday 18th January 2017-  Linux Command Line & Shell scripting

Icon 2017_01_18_CLI_Shell_Scripting.pdf (1.3 MB)

Icon Bash Scripting Cheatsheet (steve-parker.org) (PDF) (47.5 KB)

Icon The Linux Command Line, William E. Shotts, Jr (PDF Book) (2.0 MB)

Icon vi / vim cheat sheet (PDF) (27.0 KB)

Icon CLI.tar.gz (33.3 MB)


Wednesday 11th January 2017- Slurm Job Scheduler

Icon 2017_01_11_SLURM_JOB_Scheduler.pdf Clear (2.0 MB)

Icon slurm-demo (7.0 MB)


Wednesday 4th January 2017- Introduction to BioHPC, new user training

Icon 2017_01_04_BioHPC_Introduction (3.3 MB)

Icon hello_user.py (188 bytes)


Wednesday 7th December - Introduction to BioHPC, new user training

Icon 2016_12_07_BioHPC_Introduction.pdf (3.2 MB)


Wednesday 16th November - Bioinformatics Training - Introduction to Microbiome ‘Omics' Technologies

Icon 2016_11_16_Introduction_To_Microbiome.pdf (4.8 MB)


Wednesday 9th November - BioHPC Cloud Storage & Backup

Icon 2016_11_09_Cloud_Storage_Backup.pdf (1.9 MB)


 

Wednesday 2nd November - Introduction to BioHPC, new user training

Icon 2016-11-02_BioHPC_Introduction.pdf (3.3 MB)

Icon hello_user.py (194 bytes)

 


Wednseday 26th October - A Practical Guide to Integrative Genomics by RNA-seq and ChIP-seq Analysis

Icon 2016-10-26-Integrative_Genomics (3.6 MB)

 


Wednseday 19th October - Python for Scientific Developing

Icon 2016_10_19_python_for_scientific_develping (2.1 MB)

Icon ipython_notebook_examples (1.9 MB)

 


Wednseday 12th October - CUDA on BioHPC, Applications and Parallel Programming with GPUs

Icon 2016_10_11_CUDA.pdf (2.8 MB)

Icon cuda_demos.tar.gz (389.2 KB)

 


Wednesday 5th October - Introduction to BioHPC, new user training

Icon 2016_10_05_BioHPC_Introduction.pdf (3.1 MB)

 


Wednesday 28th September - Bioinformatics Training - Run Sequence Analysis Pipelines and Visualize your Data on the BioHPC

Icon bc_rnaseq_analysis_BLC.pdf (2.1 MB)


Wednesday 21st September - MATLAB on BioHPC

Icon 2016_09_21_Matlab_BioHPC.pdf (3.0 MB)

Icon matlab_demo.zip (2.6 MB)

 


Wednesday 14th September - Workstations and Thin Clients

Icon 2016-09-14_BioHPC_Workstation_and_Thin_Clients (2.1 MB)

 


Wednesday 7th September - Introduction to BioHPC, new user training

Icon 2016-09-07_BioHPC_Introduction.pdf (3.3 MB)

Icon 2016-09-07_hello_user (194 bytes)


Wednesday 24th August - Green Center Computational Core: ChIP-seq Pipeline Just a Click Away

Icon GCRB_Pipelines.pdf (7.0 MB)

 


Wednesday 17th August - Galaxy on BioHPC

Icon 20160815_Galaxy.pdf (1.9 MB)

 


Wednesday 10th August - BioHPC Cloud Storage & Backup

Icon 2016_08_10_Cloud_Storage_Backup.pdf (2.1 MB)


 

Wednesday 3rd August - Introduction to BioHPC, new user training

Icon 2016-08-03_BioHPC_Introduction.pdf (3.1 MB)

Icon 2016-08-03-hello_user.py (194 bytes)


Wednesday 27th July - Introduction to ClipSeq

Icon 2016_07_27_Introduction_to_ClipSeq_Analysis.pdf (2.5 MB)


Wednesday 20th July - Visualization on BioHPC

Icon 2016_07_20_BioHPC_Visualization.pdf (2.9 MB)

Icon visualization_demo_2016.zip (3.2 KB)


 

Wednesday 7th July - Introduction To BioHPC

Icon 2016-07-06_BioHPC_Introduction.pdf (3.1 MB)

Icon 2016-07-06_hello_user.py (194 bytes)


Wednesday 21st June - Introduction to Genetic Variation - Presented by BICF

Icon Introduction_to_genetic_variation.pdf (3.7 MB)

 


 

Wednesday 15th June - Big Data & Parallel Frameworks -  Hadoop and Spark on BioHPC

Icon 2016_06_15_Parallel_Frameworks_Big_Data.pdf (1.5 MB)
Icon 2016_06_15_hadoop_spark_examples.zip (15.2 MB)

 


Wednesday 8th June - Using the SLURM Job Scheduler (Updated)

Icon 2016_06_08_SLURM_JOB_Scheduler.pdf (1.8 MB)

Icon slurm_demo_0608.zip (6.1 MB)

 


Wednesday 1st June - Introduction to BioHPC

Icon 2016_06_01_BioHPC_Introduction.pdf (3.7 MB)


Wednesday 25th May - Sequencing Technologies (Presented by BICF)

Icon 2016_05_25_sequencingtechnologies.pdf (5.2 MB)


Wednesday 18th May - Astrocyte, the BioHPC Workflow Platform

Icon 2016_05_18_Astrocyte.pdf (2.5 MB)


Wednesday 11th May - Academic Information Resources / Texas Advance Computing Center (TACC)

Presented by Thomas Spencer (UTSW AIR) and Brian Beck (TACC Liaison)

Icon AIR / Research Software Core (214.1 KB)
Icon Introduction to TACC (1.1 MB)


Wednesday 4th May - Introduction to BioHPC

Icon 2016_05_04_BioHPC_Introduction.pdf (3.4 MB)


Wednesday 27th April - Sequence Homology and Analysis

Icon 2016_04_27_Sequence_Alignment.pdf (4.4 MB)


Wednesday 20th April - R for Bioinformatics on BioHPC

Icon R on BioHPC Slides (pdf) (1.8 MB)

Icon R example code (zip) (3.7 MB)


Wednesday 13th April - The Linux Command Line & Shell Scripting

Icon 2016_04_13_CLI_Shell_Scripting.pdf (1.3 MB)

Icon Bash Scripting Cheatsheet (steve-parker.org) (PDF) (47.5 KB)

Icon The Linux Command Line, William E. Shotts, Jr (PDF Book) (2.0 MB)

Icon vi / vim cheat sheet (PDF) (27.0 KB)

CLI.tar.gz (Download and extract with 'tar zxf CLI.tar.gz')

 


Wednesday 23rd March - Introduction to Statistical Testing, hosted by BICF

Icon Introduction to Statistical Testing (pdf) (5.8 MB)


Wednesday 16th March - BioHPC NGS Analysis Web Toolkit

Icon BioHPC Next Generation Sequencing Analysis Web Toolkit (1.5 MB)

Icon Next Generation Sequencing Web Toolkit Training Notes (1.2 MB)


Wednesday 9th March - BioHPC Cloud Storage & Backup

Icon 2016_03_07_Cloud_Storage_Backup.pdf (2.1 MB)


Wednesday 24th February - Bioinformatics Topics - Advanced Neuroscience Imaging Research on the BioHPC

Icon Advanced Neuroscience Imaging Research on the BioHPC (1.9 MB)


Wednesday 17th February - Introduction to BICF (Bioinformatics Core Facility)

Icon Introduction to BICF.pptx (4.3 MB)


Wednesday 10th February - Using the SLURM Job Scheduler (Updated)

Icon 2016_02_10_slurm_training (1.7 MB)


Wednesday 27th January - Advancing your science via collaboration with the BioHPC, Assaf Zaritsky, Danuser Lab

Icon BioHPC_20160127.pdf (2.0 MB)


Wednesday 20th January - Git Version Control

Icon 2016_01_20_Git_Training.pdf (1.5 MB)
Icon 2015_03_08_Git_Demo_Script.pdf (470.3 KB)


Wednesday 13th January - Workstations and Thin Clients

Icon workstation presentation5.pdf (2.4 MB)


Wednesday 18th November - Parallel Frameworks & Big Data - Hadoop and Spark on BioHPC

Icon 2015_10_21_Parallel_Frameworks_Big_Data.pdf (1.6 MB)

Icon hadoop_spark_examples.tar.gz (16.6 MB)


Wednesday 11th November - Using the SLURM Job Scheduler (Updated)

Icon Wednesday 11th November - Using the SLURM Job Scheduler (Updated) (1.7 MB)

Icon slurm-demo_1111.tar (38.0 MB)


Wednesday 7th October - Introduction to BioHPC

Icon 2015_10_07_BioHPC_Introduction.pdf (4.0 MB)


Wednesday 16th September - Visualization on BioHPC

Icon Wednesday 16th September - Visualization on BioHPC (Slides) (3.3 MB)


Wednesday 19th August - CUDA on BioHPC: Applications and GPU Programming

Icon Wednesday 19th August - CUDA on BioHPC (2.6 MB)
Icon Example code and executables (.tar.gz) (389.2 KB)


Wednesday 15th July - R on BioHPC

Icon Wednesday 15th July - R on BioHPC Slides (PDF) (2.0 MB)
Icon R Example Scripts and Guides (.zip) (3.7 MB)


Wednesday 17th June - MATLAB on BioHPC

Icon Wednesday 17th June - Matlab on BioHPC (2.8 MB)


Wednesday 10th June - BioHPC Cloud Storage (updated)

Icon Wednesday 10th June - BioHPC Cloud Storage (updated) (1.9 MB)


Wednesday 3rd June - Introduction to BioHPC

Icon 2015_06_03_BioHPC_Introduction.pdf (3.2 MB)


Wednesday 20th May - Python on BioHPC

Icon 2015_05_20_Python_on_BioHPC.pdf (2.1 MB)
Icon python_on_biohpc.zip (1.1 MB)


Wednesday 13rd May - Using the SLURM Job Scheduler (Updated)


Icon 2015_05_13_SLURM_JOB_Scheduler.pdf (1.7 MB)


 

Wednesday 6th May - Introduction to BioHPC (Updated)

Icon 2015_05_06_BioHPC_Introduction.pdf (3.0 MB)


Wednesday 15th April - Introduction to Next Generation Sequencing Analysis on BioHPC

Icon April 15th 2015 - NGS Analysis on BioHPC (Slides) (1.2 MB)

Icon NGS Pipeline Tutorial (1.4 MB)

Icon BioHPC Galaxy Notes (528.4 KB)


Wednesday 14th October - Workstations and Thin Clients

Icon Workstations and Thin Clients (1.8 MB)


Wednesday 18th Mar - Git Version Control

Icon 2015_03_18_Git_Training.pdf (1.7 MB)

Icon 2015_03_08_Git_Demo_Script.pdf (470.3 KB)

Atlassian Git Cheat Sheet


Wednesday 11th Mar - Using BioHPC Cloud Storage

Icon Using BioHPC Cloud Storage (1.8 MB)


Wednesday 18th Feb - The Linux Command Line & Shell Scripting

Icon 2015_02_18_CLI_Shell_Scripting.pdf (1017.7 KB)

Icon Example Bash Scripts (895 bytes)   Download and extract with 'tar zxf cli_scripts.tar.gz'

Icon Linux Command Line Cheat Sheet (Courtesy FOSSwire.com) (PDF) (69.1 KB)

Icon Bash Scripting Cheatsheet (steve-parker.org) (PDF) (47.5 KB)

Icon The Linux Command Line, William E. Shotts, Jr (PDF Book) (2.0 MB)

Icon vi / vim cheat sheet (PDF) (27.0 KB)


Wednesday 11th Feb - Using the SLURM Job Scheduler

Icon February 3nd 2015 - Slurm Job Scheduler (1.5 MB)

Icon February 3nd 2015 - Slurm job Scheduler (Demo Files) (13.7 MB)


Wednesday 4th Feb - Introduction to BioHPC

Icon February 2nd 2015 - Introduction to BioHPC (6.1 MB)