From d482023d759fbc5eef1851c2d857618e12bf5ff9 Mon Sep 17 00:00:00 2001 From: Natalie Elphick Date: Fri, 12 Apr 2024 17:32:41 -0700 Subject: [PATCH] final edits --- docs/Working_on_Wynton_Part_1.html | 65 +++-- docs/Working_on_Wynton_Part_2.html | 25 +- .../Working_on_Wynton_Part_1.Rmd | 252 ++++++++---------- .../Working_on_Wynton_Part_2.Rmd | 21 +- 4 files changed, 189 insertions(+), 174 deletions(-) diff --git a/docs/Working_on_Wynton_Part_1.html b/docs/Working_on_Wynton_Part_1.html index 98066a3..13f2af2 100644 --- a/docs/Working_on_Wynton_Part_1.html +++ b/docs/Working_on_Wynton_Part_1.html @@ -585,10 +585,16 @@ document.addEventListener('DOMContentLoaded', function(e) {

Introductions

-

Natalie Elphick
-Bioinformatician I

-

Alex Pico (TA)
-Bioinformatics Core Director

+

Instructor:

+

      Natalie Elphick
+      Bioinformatician I

+

TAs:

+

      Alex Pico
+      Bioinformatics Core Director
+      Ayushi Agrawal
+      Bioinformatician III
+      Min-Gyoung Shin
+      Bioinformatician III

Target Audience

@@ -634,7 +640,7 @@ specifications)
  • Funded and administered cooperatively by UCSF campus IT and key research groups
    • -

    https://wynton.ucsf.edu

    +

    https://wynton.ucsf.edu

    @@ -781,8 +787,8 @@ requests
  • Certain input/output patterns can be problematic
    • -
    -

    BeeGFS - I/O patterns

    +
    +

    BeeGFS - I/O patterns

    • Anything that requires lots of metadata operations can feel slow
        @@ -791,21 +797,18 @@ and directory searches (conda)
    • Keep the number of reads and writes to a single directory to a reasonable number
      • -
    • If using conda, putting the conda application inside a Apptainer -(formerly singularity) container will result in better performance
    -
    -

    BeeGFS - Tips

    +
    +

    BeeGFS - Takehome Message

    • Prefer fewer, large files over many small ones
      • -
    • Distribute reading and writing over several directories -
        -
      • Including compute job output and error files
        • -
      • -
    • Use local scratch (/scratch) when possible
      • +
    • Distribute reading and writing over several directories
      • +
    • Use local scratch (/scratch) when possible
    • Don’t include anything in /wynton in your default LD_LIBRARY_PATH
      • +
    • If using conda, putting the conda application inside a Apptainer +(formerly singularity) container will result in better performance
    @@ -872,18 +875,22 @@ contacting Gladstone IT
    knowledge base page
    -
    -

    Storage Advice

    +
    +

    Storage Advice

    • Always back up anything you store under /wynton
      • -
    • Back up your data on /gladstone if you have access -to it +
    • If you have access to it keep all of your data on +/gladstone
        -
      • A large number of jobs reading and writing to these directories will +
      • A large number of jobs reading and writing to these directories may be slower since it is NFS mounted not BeeGFS
      • -
    • Use the scratch directories to store temporary files
      • +
    • Use the scratch directories to store temporary files +
        +
      • e.g. A large amount of .fastq that you do not need after the +alignment step
        • +
    @@ -906,6 +913,13 @@ be slower since it is NFS mounted not BeeGFS 
    {local}$ scp alice@dt1.wynton.ucsf.edu:/path/to/local_file.tsv /destination/path
    +
    +

    Hands-on

    +
      +
    • Use scp to copy this file +into your home directory on Wynton
      • +
    +

    GUI SFTP Clients

      @@ -955,8 +969,7 @@ UCSF Box instructions

    Poll 1

    -

    Which of these can you not log in to from your -computer?

    +

    Poll 1 - Which of these can you not SSH in to?

    1. Login Nodes
    2. Development Nodes
      3. @@ -967,7 +980,7 @@ computer?

      Poll 2

      The /wynton directory is backed up on a nightly -basis so do not need to back up the data you store here.

      +basis, so there is no need to back up anything stored here.

      1. True
      2. False
        3. @@ -1136,7 +1149,7 @@ run:
      diff --git a/docs/Working_on_Wynton_Part_2.html b/docs/Working_on_Wynton_Part_2.html index 1d5b705..1984afa 100644 --- a/docs/Working_on_Wynton_Part_2.html +++ b/docs/Working_on_Wynton_Part_2.html @@ -585,10 +585,14 @@ document.addEventListener('DOMContentLoaded', function(e) {

      Introductions

      -

      Natalie Elphick
      -Bioinformatician I

      -

      Alex Pico (TA)
      -Bioinformatics Core Director

      +

      Instructor:

      +

            Natalie Elphick
      +      Bioinformatician I

      +

      TAs:

      +

            Alex Pico
      +      Bioinformatics Core Director
      +      Michela Traglia
      +      Senior Statistician

      Target Audience

      @@ -939,8 +943,8 @@ cancelled

      Poll 3

      -

      Anything that you can run on a compute node can be run on a -development node.

      +

      Any submitted job to compute nodes can also be run on development +nodes.

      1. True
      2. False
        3. @@ -1155,6 +1159,8 @@ into Wynton

      Bioinformatics Questions

      +

      For any bioinformatics specific questions feel free to reach out to +the Gladstone Bioinformatics Core.

      • Email
          @@ -1174,8 +1180,11 @@ into Wynton

          Thank You!

          diff --git a/working-on-wynton-hpc/Working_on_Wynton_Part_1.Rmd b/working-on-wynton-hpc/Working_on_Wynton_Part_1.Rmd index f20e2ac..6d84bd2 100644 --- a/working-on-wynton-hpc/Working_on_Wynton_Part_1.Rmd +++ b/working-on-wynton-hpc/Working_on_Wynton_Part_1.Rmd @@ -25,50 +25,50 @@ output:
          *Press the ? key for tips on navigating these slides*
          ## Introductions +Instructor: -**Natalie Elphick** -Bioinformatician I +      **Natalie Elphick** +      *Bioinformatician I* -**Alex Pico (TA)** -Bioinformatics Core Director +TAs: + +      **Alex Pico** +      *Bioinformatics Core Director* +      **Ayushi Agrawal** +      *Bioinformatician III* +      **Min-Gyoung Shin** +      *Bioinformatician III* ## Target Audience -- Prior experience with UNIX command-line - +- Prior experience with UNIX command-line ## Part 1: -1. What is an HPC cluster? -2. Node Types and Logging in -3. Storage -4. Data Transfer -5. Installing Software -6. Containers - - +1. What is an HPC cluster? +2. Node Types and Logging in +3. Storage +4. Data Transfer +5. Installing Software +6. Containers # What is Wynton HPC? ## High-performance Computing Cluster {.smaller-picture} -- A collection of specialized computers (nodes) connected together on a fast local network +- A collection of specialized computers (nodes) connected together on a fast local network ![HPC Diagram](slide_materials/HPC_diagram.png) - - ## Wynton {.small-bullets} -- A HPC Linux environment available to all UCSF researchers for free +- A HPC Linux environment available to all UCSF researchers for free\ - Uses the Rocky 8 linux OS -- Includes several hundred compute nodes and a large shared storage system ([Cluster specifications](https://wynton.ucsf.edu/hpc/about/specs.html)) -- Funded and administered cooperatively by UCSF campus IT and key research groups - -[https://wynton.ucsf.edu](https://wynton.ucsf.edu) - +- Includes several hundred compute nodes and a large shared storage system ([Cluster specifications](https://wynton.ucsf.edu/hpc/about/specs.html))\ +- Funded and administered cooperatively by UCSF campus IT and key research groups + # Node Types and Logging in @@ -86,15 +86,14 @@ Bioinformatics Core Director - The primary method to log in is to use an SSH client application - The Wynton HPC is up to date with information on logging in: [Access Cluster](https://wynton.ucsf.edu/hpc/get-started/access-cluster.html) -Names: - - +Names: + log1, log2 and plog (for PHI users) ## Login {.small-bullets} -- Connect to the UCSF or Gladstone WiFi networks (or the respective VPN) or using [2FA](https://wynton.ucsf.edu/hpc/get-started/duo-signup.html) -- **ssh [your-username]@[node].wynton.ucsf.edu** +- Connect to the UCSF or Gladstone WiFi networks (or the respective VPN) or using [2FA](https://wynton.ucsf.edu/hpc/get-started/duo-signup.html)\ +- **ssh [your-username]\@[node].wynton.ucsf.edu** ```{r, engine='bash', eval=TRUE, results='markup',comment=NA, highlight=TRUE, echo=FALSE} echo "{local}$ ssh alice@log1.wynton.ucsf.edu @@ -104,20 +103,20 @@ alice@log1.wynton.ucsf.edu's password: - There will not be any visual feedback when typing your password - ## The Development Nodes {.small-bullets} - Has a set of [core software](https://wynton.ucsf.edu/hpc/software/core-software.html) installed - - e.g. git, vim, nano, make and python + - e.g. git, vim, nano, make and python - Also has access to [software repositories](https://wynton.ucsf.edu/hpc/software/software-repositories.html) some which are maintained by other users or research groups - - e.g. matlab, R and openjdk + - e.g. matlab, R and openjdk - Cannot be logged in to directly, only from a login node + ```{r, engine='bash', eval=TRUE, results='markup',comment=NA, highlight=TRUE, echo=FALSE} echo "ssh dev1" ``` -Names: - +Names: + dev[1-3], gpudev1, pdev1 (PHI) and pgpudev1 (PHI) ## Data Transfer Nodes {.small-bullets} @@ -127,88 +126,81 @@ dev[1-3], gpudev1, pdev1 (PHI) and pgpudev1 (PHI) - Limited software - Use for transferring files to and from Wynton -Example: +Example: ```{r, engine='bash', eval=TRUE, results='markup',comment=NA, highlight=TRUE, echo=FALSE} echo "{local}$ scp local_file.tsv alice@dt1.wynton.ucsf.edu:~/" ``` -Names: - +Names: + dt1 and dt2 - - ## Compute Nodes {.small-bullets} - Can **not** be logged in to directly -- No internet or UCSF network access +- No internet or UCSF network access\ - Used to run non-interactive compute job scripts - The software to run the job script is provided using a container - ![Compute Jobs](slide_materials/compute_job_workflow.png) - - # Storage - ## The File System {.small-bullets} - A file system how information is stored and retrieved on a computer - - Consists of files and directories + - Consists of files and directories - A local file system is function of the operating system and only accessible from a single computer - A shared file system is accessible from multiple computers - - ## BeeGFS {.small-bullets} - Wynton uses a *parallel* shared file system called BeeGFS - - The files are stored as "chunks" spread across many different servers + - The files are stored as "chunks" spread across many different servers - BeeGFS has multiple services that work together to manage the file system - - Storage (stores the chunks) - - Metadata (tracks the chunks and information about their file) - - Management (tracks all of the services) - - Client (provides linux access to the file system) - + - Storage (stores the chunks) + - Metadata (tracks the chunks and information about their file) + - Management (tracks all of the services) + - Client (provides linux access to the file system) + +## BeeGFS - Advantages -## BeeGFS - Advantages - High throughput - Redundancy can be built in by mirroring services - Adding new storage is fast and does not require downtime -## BeeGFS - Caveats +## BeeGFS - Caveats + - For any client node, performance is limited by the network bandwidth of that node - Network latency becomes extremely important for all metadata requests - Certain input/output patterns can be problematic -## BeeGFS - I/O patterns {.small-bullets} -- Anything that requires lots of metadata operations can feel slow +## BeeGFS - I/O patterns + +- Anything that requires lots of metadata operations can feel slow - e.g: lots of writes to the same directory and lots of file lookups and directory searches (**conda**) - Keep the number of reads and writes to a single directory to a reasonable number -- If using conda, putting the conda application inside a Apptainer (formerly singularity) container will result in better performance -## BeeGFS - Tips + +## BeeGFS - Takehome Message {.small-bullets} - Prefer fewer, large files over many small ones - Distribute reading and writing over several directories - - Including compute job output and error files - Use local scratch (**/scratch**) when possible - Don't include anything in **/wynton** in your default LD_LIBRARY_PATH - +- If using conda, putting the conda application inside a Apptainer (formerly singularity) container will result in better performance ## Storage {.small-bullets} - **Wynton storage is not backed up** - /wynton/home/**[group_name]**/**[user]** - - PHI users : /wynton/protected/home/**[group_name]**/**[user]** - - User home directory - limited to 500 GiB + - PHI users : /wynton/protected/home/**[group_name]**/**[user]** + - User home directory - limited to 500 GiB - /wynton/group/**[group_name]** - - PHI users : /wynton/protected/group/**[group_name]** - - User group directory - disk quota varies by group - - Use this directory for any analysis you want to share with your lab + - PHI users : /wynton/protected/group/**[group_name]** + - User group directory - disk quota varies by group + - Use this directory for any analysis you want to share with your lab - [More information on disk quotas](https://wynton.ucsf.edu/hpc/howto/storage-size.html#file-sizes-and-disk-quotas) To check your group disk quota run: @@ -217,76 +209,79 @@ To check your group disk quota run: echo 'beegfs-ctl --getquota --storagepoolid=12 --gid "$(id --group)"' ``` - - ## Scratch - Temporary Storage {.small-bullets} + - Local **/scratch** - 0.1-1.8 TiB/node storage unique to each compute node - Can only be accessed from the specific compute node - - Use this to store intermediate files only needed for a job + - Use this to store intermediate files only needed for a job\ - **/wynton/scratch** and **/wynton/protected/scratch** (for PHI users) - 703 TiB storage accessible from everywhere - No quotas - -

          - + +

          + **Files not used for 2 weeks are automatically deleted** - - ## Gladstone HIVE + - Gladstone's HIVE storage server is mounted directly to Wynton under **/gladstone** - Only certain HIVE folders are accessible directly on Wynton - Files under **/gladstone** are backed up - Naming: **/gladstone/[lab]** - - Directories that are shared between multiple labs can be set up by contacting Gladstone IT + - Directories that are shared between multiple labs can be set up by contacting Gladstone IT\ - For more information visit the [IT knowledge base page](https://help.gladstone.org/support/solutions/articles/14000033963) - -## Storage Advice +## Storage Advice {.small-bullets} - Always back up anything you store under **/wynton** -- Back up your data on **/gladstone** if you have access to it - - A large number of jobs reading and writing to these directories will be slower since it is NFS mounted not BeeGFS +- If you have access to it keep all of your data on **/gladstone** + - A large number of jobs reading and writing to these directories may be slower since it is NFS mounted not BeeGFS - Use the scratch directories to store temporary files - - + - e.g. A large amount of .fastq that you do not need after the alignment step # Data Transfer - - ## Secure Copy - scp - Local file to Wynton + ```{r, engine='bash', eval=TRUE, results='markup',comment=NA, highlight=TRUE, echo=FALSE} echo "{local}$ scp /path/to/local_file.tsv alice@dt1.wynton.ucsf.edu:/destination/path" ``` - Copy a directory to a folder on Wynton + ```{r, engine='bash', eval=TRUE, results='markup',comment=NA, highlight=TRUE, echo=FALSE} echo "{local}$ scp -r local_folder/ alice@dt1.wynton.ucsf.edu:/destination/path" ``` - Copy a single file to Wynton from your local machine + ```{r, engine='bash', eval=TRUE, results='markup',comment=NA, highlight=TRUE, echo=FALSE} echo "{local}$ scp alice@dt1.wynton.ucsf.edu:/path/to/local_file.tsv /destination/path" ``` +## Hands-on + +- Use scp to copy this [file](https://www.dropbox.com/scl/fi/463ymz88q89d2co90kj30/candidatus_carsonella_ruddii_complete_genome.fasta?rlkey=9x64iek2yy149sh2i1r9sse9y&dl=1) into your home directory on Wynton + + + + + ## GUI SFTP Clients {.small-bullets} - These let you transfer files to and from Wynton using a GUI - [2 factor authentication](https://wynton.ucsf.edu/hpc/get-started/duo-signup.html) may be required -- [Cyberduck](https://cyberduck.io/) - - Navigate to Preferences -> Transfers -> General +- [Cyberduck](https://cyberduck.io/) + - Navigate to Preferences -\> Transfers -\> General - change the Transfer Files setting "Use browser connection" instead of "Open Multiple connections" - -- [FileZilla](https://filezilla-project.org/) +- [FileZilla](https://filezilla-project.org/) - In the General tab, select ‘SFTP’ as the Protocol instead of ‘FTP’ - For Logon Type, select ‘Interactive’ instead of ‘Ask for Password’ - Under the Transfer Settings tab, you might need to click the ‘Limit number of simultaneous connections’ and make sure the ‘Maximum number of connections’ is set to 1 - ## Globus - [Globus](https://wynton.ucsf.edu/hpc/transfers/globus.html) is a service for moving, syncing, and sharing large amounts of data @@ -300,27 +295,21 @@ echo "{local}$ scp alice@dt1.wynton.ucsf.edu:/path/to/local_file.tsv /destinatio - Do this from a data transfer node using screen/tmux - Do not use rclone for transfers to Box, follow the [Wynton to UCSF Box](https://wynton.ucsf.edu/hpc/transfers/ucsf-box.html) instructions +## Poll 1 +Poll 1 - Which of these can you **not** SSH in to? - -## Poll 1 - -Which of these can you **not** log in to from your computer? - -1. Login Nodes -2. Development Nodes -3. Data transfer Nodes -4. Compute Nodes +1. Login Nodes +2. Development Nodes +3. Data transfer Nodes +4. Compute Nodes ## Poll 2 -The **/wynton** directory is backed up on a nightly basis so do not need to back up the data you store here. - -1. True -2. False - - +The **/wynton** directory is backed up on a nightly basis, so there is no need to back up anything stored here. +1. True +2. False # Installing Software @@ -331,9 +320,9 @@ The **/wynton** directory is backed up on a nightly basis so do not need to back - Always install software in a development node - Download a precompiled binary or [install from source](https://wynton.ucsf.edu/hpc/howto/install-from-source.html) -## Install Samtools from Source {.small-list} +## Install Samtools from Source {.small-list} -1. Download and extract source code +1. Download and extract source code ```{r, engine='bash', eval=TRUE, results='markup',comment=NA, highlight=TRUE, echo=FALSE} echo '[alice@dev1 ~]$ mkdir -p "/scratch/$USER" @@ -342,13 +331,14 @@ echo '[alice@dev1 ~]$ mkdir -p "/scratch/$USER" [alice@dev1 alice]$ tar -x -f samtools-1.19.2.tar.bz2' ``` -2. Create install location and configure +2. Create install location and configure ```{r, engine='bash', eval=TRUE, results='markup',comment=NA, highlight=TRUE, echo=FALSE} echo '[alice@dev1 ~]$ mkdir -p $HOME/software/samtools-1.14' echo '[alice@dev1 ~]$ ./configure --prefix=$HOME/software/samtools-1.14' ``` -3. Build and install + +3. Build and install ```{r, engine='bash', eval=TRUE, results='markup',comment=NA, highlight=TRUE, echo=FALSE} echo '[alice@dev1 ~]$ make' @@ -358,9 +348,8 @@ echo '[alice@dev1 ~]$ make install' ## Install Nextflow - Scientific workflow system with a community maintained set of [core bioinformatics analysis](https://nf-co.re/) pipelines - - We will cover an example RNA-seq pipeline in part 2 -- These can be configured to use the Wynton compute job submission system - + - We will cover an example RNA-seq pipeline in part 2\ +- These can be configured to use the Wynton compute job submission system ```{r, engine='bash', eval=TRUE, results='markup',comment=NA, highlight=TRUE, echo=FALSE} echo '[alice@dev1 ~]$ cd ~/software' @@ -372,11 +361,8 @@ echo '[alice@dev1 ~]$ wget -qO- https://get.nextflow.io | bash' echo '[alice@dev1 ~]$ nextflow -v' ``` - - # Containers - ## Motivation {.small-bullets .small-picture} - Compute heavy jobs (high RAM, multiple cores) should be run on compute nodes @@ -386,25 +372,28 @@ echo '[alice@dev1 ~]$ nextflow -v' ![Compute Jobs](slide_materials/compute_job_workflow.png) - ## Definitions {.small-bullets} - **Containers:** An isolated environment for running software that is created from an *image* file, preventing conflicts with the host system. -- **Images:** An ordered collection of root filesystem changes that contain all necessary dependencies, ensuring software run identically across various computing platforms. - +- **Images:** An ordered collection of root filesystem changes that contain all necessary dependencies, ensuring software run identically across various computing platforms. ## Apptainer {.small-bullets} -- Wynton supports [Apptainer](https://wynton.ucsf.edu/hpc/software/apptainer.html) (formerly singularity) containers +- Wynton supports [Apptainer](https://wynton.ucsf.edu/hpc/software/apptainer.html) (formerly singularity) containers + - [Docker](https://docs.docker.com/) is a commonly used image creation software, these can be turned into apptainer image files (.sif) easily - apptainer run - - Run predefined script within container -- apptainer exec - - Execute any command within container -- apptainer shell - - Run bash shell within container + - Run predefined script within container + +- apptainer exec + + - Execute any command within container + +- apptainer shell + + - Run bash shell within container ## Example Container - Hello World @@ -414,7 +403,7 @@ echo '[alice@dev1 ~]$ nextflow -v' echo '[alice@dev1 ~]$ apptainer pull docker://natalie23gill/hello-world:1.0' ``` -- Execute the "hi" command in the container +- Execute the "hi" command in the container ```{r, engine='bash', eval=TRUE, results='markup',comment=NA, highlight=TRUE, echo=FALSE} echo '[alice@dev1 ~]$ apptainer exec hello-world_1.0.sif hi' @@ -428,7 +417,6 @@ echo ' __ __ ____ _ __ __ __ __ /_/ /_/\___/_/_/\____/ |__/|__/\____/_/ /_/\__,_/ (_) ' ``` - ## Example Container - This container has **figlet** installed which creates ASCII art from text input @@ -451,28 +439,22 @@ echo '[alice@dev1 ~]$ apptainer exec hello-world_1.0.sif figlet your_text' echo '[alice@dev1 ~]$ apptainer exec hello-world_1.0.sif cat /Dockerfile' ``` - # End of Part 1 ## Thank You! -- Please take some time to fill out the workshop survey if you are not attending part 2: -[https://www.surveymonkey.com/r/F75J6VZ](https://www.surveymonkey.com/r/F75J6VZ) - +- Please take some time to fill out the workshop survey if you are not attending part 2:\ + ## Upcoming Data Science Training Program Workshops - -[Introduction to Linear Mixed Effects Models](https://gladstone.org/events/introduction-linear-mixed-effects-models) +[Introduction to Linear Mixed Effects Models](https://gladstone.org/events/introduction-linear-mixed-effects-models)\ April 25-April 26, 2024 1-3pm PDT -[Single Cell RNA-Seq Data Analysis](https://gladstone.org/events/single-cell-rna-seq-data-analysis) +[Single Cell RNA-Seq Data Analysis](https://gladstone.org/events/single-cell-rna-seq-data-analysis)\ April 29-April 30, 2024 9am-4pm PDT -[Single Cell ATAC-Seq Data Analysis Part 1](https://gladstone.org/events/single-cell-atac-seq-data-analysis-part-1-1) +[Single Cell ATAC-Seq Data Analysis Part 1](https://gladstone.org/events/single-cell-atac-seq-data-analysis-part-1-1)\ May 6-May 7, 2024 1-4pm PDT - -[Complete Schedule](https://gladstone.org/events?series=189) - - +[Complete Schedule](https://gladstone.org/events?series=189) diff --git a/working-on-wynton-hpc/Working_on_Wynton_Part_2.Rmd b/working-on-wynton-hpc/Working_on_Wynton_Part_2.Rmd index 523c03c..34fe4bd 100644 --- a/working-on-wynton-hpc/Working_on_Wynton_Part_2.Rmd +++ b/working-on-wynton-hpc/Working_on_Wynton_Part_2.Rmd @@ -25,12 +25,18 @@ output:
          *Press the ? key for tips on navigating these slides*
          ## Introductions +Instructor: -**Natalie Elphick** -Bioinformatician I +      **Natalie Elphick** +      *Bioinformatician I* -**Alex Pico (TA)** -Bioinformatics Core Director + +TAs: + +      **Alex Pico** +      *Bioinformatics Core Director* +      **Michela Traglia** +      *Senior Statistician* ## Target Audience @@ -244,7 +250,7 @@ Read the [querying jobs](https://wynton.ucsf.edu/hpc/scheduler/list-jobs.html) W ## Poll 3 -Anything that you can run on a compute node can be run on a development node. +Any submitted job to compute nodes can also be run on development nodes. 1. True 2. False @@ -417,6 +423,8 @@ alice1@log1.wynton.ucsf.edu:s password: XXXXXXXXXXXXXXXXXXX ## Bioinformatics Questions +For any bioinformatics specific questions feel free to reach out to the Gladstone Bioinformatics Core. + - Email - [bioinformatics@gladstone.ucsf.edu](mailto:bioinformatics@gladstone.ucsf.edu) - Slack channel #questions-about-bioinformatics @@ -431,6 +439,9 @@ alice1@log1.wynton.ucsf.edu:s password: XXXXXXXXXXXXXXXXXXX - Please take some time to fill out the workshop survey: [https://www.surveymonkey.com/r/F75J6VZ](https://www.surveymonkey.com/r/F75J6VZ) +- Want some additional Wynton training? +Check out the UCSF library [Introduction to Wynton HPC Cluster](https://calendars.library.ucsf.edu/event/12197724) Workshop + ## Upcoming Data Science Training Program Workshops