Common Workflow Language with BioExcel Building Blocks

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Common Workflow Language with BioExcel Building Blocks

Common Workflow Language with BioExcel Building Blocks

Based on the Protein MD Setup tutorial using BioExcel Building Blocks (biobb)

This tutorial aims to illustrate the process of building up a CWL workflow using the BioExcel Building Blocks library (biobb). The tutorial is based on the Protein Gromacs MD Setup Jupyter Notebook tutorial.

Biobb modules used:

  • biobb_io: Tools to fetch biomolecular data from public databases.
  • biobb_model: Tools to model macromolecular structures.
  • biobb_md: Tools to setup and run Molecular Dynamics simulations.
  • biobb_analysis: Tools to analyse Molecular Dynamics trajectories.

Software requirements:

  • cwltool: Common Workflow Language tool description reference implementation.
  • docker: Docker container platform.

Tutorial Sections:

  1. CWL workflows: Brief Introduction

  2. BioExcel building blocks TOOLS CWL Descriptions

  3. BioExcel building blocks WORKFLOWS CWL Descriptions

  4. Protein MD-Setup CWL workflow with BioExcel building blocks

  5. Questions & Comments

CWL workflows: Brief Introduction

The Common Workflow Language (CWL) is an open standard for describing analysis workflows and tools in a way that makes them portable and scalable across a variety of software and hardware environments, from workstations to cluster, cloud, and high performance computing (HPC) environments.

CWL is a community-led specification to express portable workflow and tool descriptions, which can be executed by multiple leading workflow engine implementations. Unlike previous standardisation attempts, CWL has taken a pragmatic approach and focused on what most workflow systems are able to do: Execute command line tools and pass files around in a top-to-bottom pipeline. At the heart of CWL workflows are the tool descriptions. A command line is described, with parameters, input and output files, in a YAML format so they can be shared across workflows and linked to from registries like ELIXIR’s bio.tools. These are then combined and wired together in a second YAML file to form a workflow template, which can be executed on any of the supported implementations, repeatedly and on different platforms by specifying input files and workflow parameters. The CWL User Guide gives a gentle introduction to the language, while the more detailed CWL specifications formalize CWL concepts so they can be implemented by the different workflow systems. A couple of BioExcel webinars were focused on CWL, an introduction to CWL and a new open source tool to run CWL workflows on LSF (CWLEXEC).

BioExcel building blocks are all described in CWL. A specific CWL section in the workflow manager adapters github repository gathers all the descriptions, divided in the different categories: io, md, analysis, chemistry, model and pmx (see updated table here).

In this tutorial, we are going to use these BioExcel building blocks CWL descriptions to build a CWL biomolecular workflow. In particular, the assembled workflow will perform a complete Molecular Dynamics setup (MD Setup) using GROMACS MD package, taking as a base the Protein Gromacs MD Setup Jupyter Notebook tutorial.

No additional installation is required apart from the Docker platform and the CWL tool reference executor, as the building blocks will be launched using their associated Docker containers.

BioExcel building blocks TOOLS CWL Descriptions

Writing a workflow in CWL using the BioExcel building blocks is possible thanks to the already generated CWL descriptions for all the building blocks (wrappers). A specific CWL section in the workflow manager adapters github repository gathers all the descriptions, divided in the different categories: io, md, analysis, chemistry, model and pmx (see updated table here).

Tool Building Block CWL sections:

Example: Step 1 of the workflow, download a protein structure from the PDB database. The building block used for this is the Pdb building block, from the biobb_io package, including tools to fetch biomolecular data from public databases. The CWL description for this building block can be found in the adapters github repo, and is shown in the following notebook cell. Description files like this one for all the steps of the workflow are needed to build and run a CLW workflow. To build a CWL workflow with BioExcel building blocks, one just need to download all the needed description files from the biobb_adapters github.

This particular example of a Pdb building block is useful to illustrate the most important points of the CWL description:

  • hints: The CWL hints section describes the process requirements that should (but not have to) be satisfied to run the wrapped command. The implementation may report a warning if a hint cannot be satisfied. In the BioExcel building blocks, a DockerRequirement subsection is always present in the hints section, pointing to the associated Docker container. The dockerPull: parameter takes the same value that you would pass to a docker pull command. That is, the name of the container image. In this case we have used the container called biobb_io:latest that can be found in the quay.io repository, which contains the Pdb building block.
In [ ]:
hints:
  DockerRequirement:
    dockerPull: quay.io/biocontainers/biobb_io:latest
  • namespaces and schemas: Input and output metadata may be represented within a tool or workflow. Such metadata must use a namespace prefix listed in the $namespaces and $schemas sections of the document. All BioExcel building blocks CWL specifications use the EDAM ontology (http://edamontology.org/) as namespace, with all terms included in its Web Ontology Language (owl) of knowledge representation (http://edamontology.org/EDAM_1.22.owl). BioExcel is contributing to the expansion of the EDAM ontology with the addition of new structural terms such as GROMACS XTC format or the trajectory visualization operation.
In [ ]:
$namespaces:
  edam: http://edamontology.org/
$schemas:
  - http://edamontology.org/EDAM_1.22.owl
  • inputs: The inputs section of a tool contains a list of input parameters that control how to run the tool. Each parameter has an id for the name of parameter, and type describing what types of values are valid for that parameter. Available primitive types are string, int, long, float, double, and null; complex types are array and record; in addition there are special types File, Directory and Any. The field inputBinding is optional and indicates whether and how the input parameter should appear on the tool’s command line, in which position (position), and with which name (prefix). The default field stores the default value for the particular input parameter.
    In this particular example, the Pdb building block has two different input parameters: output_pdb_path and config. The output_pdb_path input parameter defines the name of the output file that will contain the downloaded PDB structure. The config parameter is common to all BioExcel building blocks, and gathers all the properties of the building block in a json format. The question mark after the string type (string?) denotes that this input is optional.
In [ ]:
inputs:
  output_pdb_path:
    type: string
    inputBinding:
      position: 1
      prefix: --output_pdb_path
    default: 'downloaded_structure.pdb'

  config:
    type: string?
    inputBinding:
      position: 2
      prefix: --config
    default: '{"pdb_code" : "1aki"}'
  • outputs: The outputs section of a tool contains a list of output parameters that should be returned after running the tool. Similarly to the inputs section, each parameter has an id for the name of parameter, and type describing what types of values are valid for that parameter. The outputBinding field describes how to set the value of each output parameter. The glob field consists of the name of a file in the output directory. In the BioExcel building blocks, every output has an associated input parameter defined in the previous input section, defining the name of the file to be generated.
    In the particular Pdb building block example, the output_pdb_file parameter of type File is coupled to the output_pdb_path input parameter, using the outputBinding and the glob fields. The standard PDB format of the output file is also specified using the EDAM ontology format id 1476 (edam:format_1476).
In [ ]:
outputs:
  output_pdb_file:
    type: File
    format: edam:format_1476
    outputBinding:
      glob: $(inputs.output_pdb_path)

For more information on CWL tools description, please refer to the CWL User Guide or the CWL specifications.

Complete Pdb Building Block CWL description:

Example of a BioExcel building block CWL description (pdb from biobb_io package)

In [ ]:
# Example of a BioExcel building block CWL description (pdb from biobb_io package)

#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: CommandLineTool
baseCommand: pdb
hints:
  DockerRequirement:
    dockerPull: quay.io/biocontainers/biobb_io:latest
            
inputs:
  output_pdb_path:
    type: string
    inputBinding:
      position: 1
      prefix: --output_pdb_path
    default: 'downloaded_structure.pdb'

  config:
    type: string?
    inputBinding:
      position: 2
      prefix: --config
    default: '{"pdb_code" : "1aki"}'
       
outputs:
  output_pdb_file:
    type: File
    format: edam:format_1476
    outputBinding:
      glob: $(inputs.output_pdb_path)

$namespaces:
  edam: http://edamontology.org/
$schemas:
  - http://edamontology.org/EDAM_1.22.owl

BioExcel building blocks WORKFLOWS CWL Descriptions

Now that we have seen the BioExcel building blocks CWL descriptions, we can use them to build our first biomolecular workflow as a demonstrator. All CWL workflows are divided in two files: the CWL description and the YAML or JSON files containing all workflow inputs. Starting with the CWL workflow description, let's explore our first example section by section.

Header:

  • cwlVersion field indicates the version of the CWL spec used by the document.
  • class field indicates this document describes a workflow.
In [ ]:
# !/usr/bin/env cwl-runner

cwlVersion: v1.0
class: Workflow
label: Example CWL Header
doc: |
  An example of how to create a CWl header. We have specified the version
  of CWL that we are using; the class, which is a 'workflow'.  The label
  field should provide a short title or description of the workflow and
  the description should provide a longer description of what the workflow
  doe.

Inputs:

The inputs section describes the inputs for each of the steps of the workflow. The BioExcel building blocks (biobb) have three types of input parameters: input, output, and properties. The properties parameter, which contains all the input parameters that are neither input nor output files, is defined in JSON format (see examples in the Protein MD Setup Jupyter Notebook tutorial).

Example: Step 1 of the workflow, download a protein structure from the PDB database. Two different inputs are needed for this step: the name of the file that will contain the downloaded PDB structure (step1_output_name), and the properties of the building block (step1_properties), that in this case will indicate the PDB code to look for (see Input of a run section). Both input parameters have type string in this building block.

In [ ]:
# CWL workflow inputs section example
inputs:
  step1_output_name: string
  step1_properties: string

Outputs:

The outputs: section describes the set of final outputs from the workflow. These outputs can be a collection of outputs from different steps of the workflow. Each output is a key: value pair. The key should be a unique identifier, and the value should be a dictionary (consisting of key: value pairs). These keys consists of label, which is a title or name for the output; doc, which is a longer description of what this output is; type, which is the data type expected; and outputSource, which connects the output parameter of a particular step to the workflow final output parameter.

In [ ]:
outputs:
  pdb: #unique identifier
    label: Protein structure  
    doc: |
      Step 1 of the workflow, download a 'protein structure' from the
      'PDB database'. The *pdb* 'output' is a 'file' containing the
      'protein structure' in 'PDB format', which is connected to the
      output parameter *output_pdb_file* of the 'step1 of the workflow'
      (*step1_pdb*).
    type: File #data type
    outputSource: step1_pdb/output_pdb_file

Steps:

The steps section describes the actual steps of the workflow. Steps are connected one to the other through the input parameters.

Workflow steps are not necessarily run in the order they are listed, instead the order is determined by the dependencies between steps. In addition, workflow steps which do not depend on one another may run in parallel.

Example: Step 1 and 2 of the workflow, download a protein structure from the PDB database, and fix the side chains, adding any side chain atoms missing in the original structure. Note how step1 and step2 are connected through the output of one and the input of the other: Step2 (step2_fixsidechain) receives as input (input_pdb_path) the output of the step1 (step1_pdb), identified as step1_pdb/output_pdb_file.

In [ ]:
# CWL workflow steps section example
  step1_pdb:
    label: Fetch PDB Structure
    doc: |
      Download a protein structure from the PDB database
    run: biobb/biobb_adapters/cwl/biobb_io/mmb_api/pdb.cwl
    in:
      output_pdb_path: step1_pdb_name
      config: step1_pdb_config
    out: [output_pdb_file]

  step2_fixsidechain:
    label: Fix Protein structure
    doc: |
      Fix the side chains, adding any side chain atoms missing in the
      original structure.
    run: biobb/biobb_adapters/cwl/biobb_model/model/fix_side_chain.cwl
    in:
      input_pdb_path: step1_pdb/output_pdb_file
    out: [output_pdb_file]

Input of a run:

As previously stated, all CWL workflows are divided in two files: the CWL description and the YAML or JSON files containing all workflow inputs. In this example, we are going to produce a YAML formatted object in a separate file describing the inputs of our run.

Example: Step 1 of the workflow, download a protein structure from the PDB database. The step1_output_name contains the name of the file that is going to be produced by the building block, whereas the JSON-formatted properties (step1_properties) contain the pdb code of the structure to be downloaded:

  • step1_output_name: "tutorial_1aki.pdb"
  • step1_properties: {"pdb_code" : "1aki"}
In [ ]:
step1_output_name: 'tutorial_1aki.pdb'
step1_properties: '{"pdb_code" : "1aki"}'

Complete workflow:

Example of a short CWL workflow with BioExcel building blocks, which retrieves a PDB file for the Lysozyme protein structure from the RCSB PDB database (step1: pdb.cwl), and fixes the possible problems in the structure, adding missing side chain atoms if needed (step2: fix_side_chain.cwl).

In [ ]:
# !/usr/bin/env cwl-runner

cwlVersion: v1.0
class: Workflow
label: Example of a short CWL workflow with BioExcel building blocks
doc: |
  Example of a short 'CWL workflow' with 'BioExcel building blocks', which
  retrieves a 'PDB file' for the 'Lysozyme protein structure' from the RCSB PDB
  database ('step1: pdb.cwl'), and fixes the possible problems in the structure,
  adding 'missing side chain atoms' if needed ('step2: fix_side_chain.cwl').

inputs:
  step1_properties: '{"pdb_code" : "1aki"}'
  step1_output_name: 'tutorial_1aki.pdb'

outputs:
  pdb:
    type: File
    outputSource: step2_fixsidechain/output_pdb_file

steps:
  step1_pdb:
    label: Fetch PDB Structure
    doc: |
      Download a protein structure from the PDB database
    run: biobb_adapters/pdb.cwl
    in:
      output_pdb_path: step1_output_name
      config: step1_properties
    out: [output_pdb_file]
        
  step2_fixsidechain:
    label: Fix Protein structure
    doc: |
      Fix the side chains, adding any side chain atoms missing in the
      original structure.
    run: biobb_adapters/fix_side_chain.cwl
    in:
      input_pdb_path: step1_pdb/output_pdb_file
    out: [output_pdb_file]

Running the CWL workflow:

The final step of the process is running the workflow described in CWL. For that, the description presented in the previous cell should be written to a file (e.g. BioExcel-CWL-firstWorkflow.cwl), the YAML input should be written to a separate file (e.g. BioExcel-CWL-firstWorkflow-job.yml) and finally both files should be used with the CWL tool description reference implementation executer (cwltool).

It is important to note that in order to properly run the CWL workflow, the CWL descriptions for all the building blocks used in the workflow should be accessible from the file system. In this example, all the CWL descriptions needed where downloaded from the BioExcel building blocks adapters github repository to a folder named biobb_adapters.

The command line is shown in the cell below:

In [ ]:
# Run CWL workflow with CWL tool description reference implementation (cwltool).
cwltool BioExcel-CWL-firstWorkflow.cwl BioExcel-CWL-firstWorkflow-job.yml

Cwltool workflow output

The execution of the workflow will write information to the standard output such as the step being performed, the way it is run (command line, docker container, etc.), inputs and outputs used, and state of each step (success, failed). The next cell contains a real output for the execution of our first example:

In [ ]:
Resolved 'BioExcel-CWL-firstWorkflow.cwl' to 'file:///PATH/biobb_wf_md_setup/cwl/BioExcel-CWL-firstWorkflow.cwl'
[workflow BioExcel-CWL-firstWorkflow.cwl] start
[step step1_pdb] start
[job step1_pdb] /private/tmp/docker_tmp1g8y0wu0$ docker \
    run \
    -i \
    --volume=/private/tmp/docker_tmp1g8y0wu0:/private/var/spool/cwl:rw \
    --volume=/private/var/folders/7f/0hxgf3d971b98lk_fps26jx40000gn/T/tmps4_pw5tj:/tmp:rw \
    --workdir=/private/var/spool/cwl \
    --read-only=true \
    --user=501:20 \
    --rm \
    --env=TMPDIR=/tmp \
    --env=HOME=/private/var/spool/cwl \
    quay.io/biocontainers/biobb_io:0.1.3--py_0 \
    pdb \
    --config \
    '{"pdb_code" : "1aki"}' \
    --output_pdb_path \
    tutorial.pdb
2019-10-24 08:42:06,235 [MainThread  ] [INFO ]  Downloading: 1aki from: https://files.rcsb.org/download/1aki.pdb
2019-10-24 08:42:07,594 [MainThread  ] [INFO ]  Writting pdb to: /private/var/spool/cwl/tutorial.pdb
2019-10-24 08:42:07,607 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'MODEL', 'ENDMDL']
[job step1_pdb] completed success
[step step1_pdb] completed success
[step step2_fixsidechain] start
[job step2_fixsidechain] /private/tmp/docker_tmpuaecttdd$ docker \
    run \
    -i \
    --volume=/private/tmp/docker_tmpuaecttdd:/private/var/spool/cwl:rw \
    --volume=/private/var/folders/7f/0hxgf3d971b98lk_fps26jx40000gn/T/tmp9t_nks8r:/tmp:rw \
    --volume=/private/tmp/docker_tmp1g8y0wu0/tutorial.pdb:/private/var/lib/cwl/stg5b2950e7-ef54-4df6-be70-677050c4c258/tutorial.pdb:ro \
    --workdir=/private/var/spool/cwl \
    --read-only=true \
    --user=501:20 \
    --rm \
    --env=TMPDIR=/tmp \
    --env=HOME=/private/var/spool/cwl \
    quay.io/biocontainers/biobb_model:0.1.3--py_0 \
    fix_side_chain \
    --input_pdb_path \
    /private/var/lib/cwl/stg5b2950e7-ef54-4df6-be70-677050c4c258/tutorial.pdb \
    --output_pdb_path \
    fixed.pdb
[job step2_fixsidechain] completed success
[step step2_fixsidechain] completed success
[workflow BioExcel-CWL-firstWorkflow.cwl] completed success
{
    "pdb": {
        "location": "file:///PATH/biobb_wf_md_setup/cwl/fixed.pdb",
        "basename": "fixed.pdb",
        "class": "File",
        "checksum": "sha1$3ef7a955f93f25af5e59b85bcf4cb1d0bbf69a40",
        "size": 81167,
        "format": "http://edamontology.org/format_1476",
        "path": "/PATH/biobb_wf_md_setup/cwl/fixed.pdb"
    }
}
Final process status is success

Protein MD-Setup CWL workflow with BioExcel building blocks

The last step of this tutorial illustrates the building of a complex CWL workflow. The example used is the Protein Gromacs MD Setup Jupyter Notebook tutorial. It is strongly recommended to take a look at this notebook before moving on to the next sections of this tutorial, as it contains information for all the building blocks used. The aim of this tutorial is to illustrate how to build CWL workflows using the BioExcel building blocks. For information about the science behind every step of the workflow, please refer to the Protein Gromacs MD Setup Jupyter Notebook tutorial. The workflow presented in the next cells is a translation of the very same workflow to CWL language, including the same number of steps (23) and building blocks.

Steps:

First of all, let's define the steps of the workflow.

  • Fetching PDB Structure: step 1
  • Fix Protein Structure: step 2
  • Create Protein System Topology: step 3
  • Create Solvent Box: step 4
  • Fill the Box with Water Molecules: step 5
  • Adding Ions: steps 6 and 7
  • Energetically Minimize the System: steps 8, 9 and 10
  • Equilibrate the System (NVT): steps 11, 12 and 13
  • Equilibrate the System (NPT): steps 14, 15 and 16
  • Free Molecular Dynamics Simulation: steps 17 and 18
  • Post-processing Resulting 3D Trajectory: steps 19 to 23

Mandatory and optional inputs and outputs of every building block can be consulted in the appropriate documentation pages from the corresponding BioExcel building block category (see updated table here).

In [ ]:
 step1_pdb:
    label: Fetch PDB Structure
    doc: |
      Download a protein structure from the PDB database
    run: biobb/biobb_adapters/cwl/biobb_io/mmb_api/pdb.cwl
    in:
      output_pdb_path: step1_pdb_name
      config: step1_pdb_config
    out: [output_pdb_file]

  step2_fixsidechain:
    label: Fix Protein structure
    doc: |
      Fix the side chains, adding any side chain atoms missing in the
      original structure.
    run: biobb/biobb_adapters/cwl/biobb_model/model/fix_side_chain.cwl
    in:
      input_pdb_path: step1_pdb/output_pdb_file
    out: [output_pdb_file]

  step3_pdb2gmx:
    label: Create Protein System Topology
    run: biobb/biobb_adapters/cwl/biobb_md/gromacs/pdb2gmx.cwl
    in:
      input_pdb_path: step2_fixsidechain/output_pdb_file
    out: [output_gro_file, output_top_zip_file]

  step4_editconf:
    label: Create Solvent Box
    run: biobb/biobb_adapters/cwl/biobb_md/gromacs/editconf.cwl
    in:
      input_gro_path: step3_pdb2gmx/output_gro_file
    out: [output_gro_file]

  step5_solvate:
    label: Fill the Box with Water Molecules
    run: biobb/biobb_adapters/cwl/biobb_md/gromacs/solvate.cwl
    in:
      input_solute_gro_path: step4_editconf/output_gro_file
      input_top_zip_path: step3_pdb2gmx/output_top_zip_file
    out: [output_gro_file, output_top_zip_file]

  step6_grompp_genion:
    label: Add Ions - part 1
    run: biobb/biobb_adapters/cwl/biobb_md/gromacs/grompp.cwl
    in:
      config: step6_gppion_config
      input_gro_path: step5_solvate/output_gro_file
      input_top_zip_path: step5_solvate/output_top_zip_file
    out: [output_tpr_file]

  step7_genion:
    label: Add Ions - part 2
    run: biobb/biobb_adapters/cwl/biobb_md/gromacs/genion.cwl
    in:
      config: step7_genion_config
      input_tpr_path: step6_grompp_genion/output_tpr_file
      input_top_zip_path: step5_solvate/output_top_zip_file
    out: [output_gro_file, output_top_zip_file]

  step8_grompp_min:
    label: Energetically Minimize the System - part 1
    run: biobb/biobb_adapters/cwl/biobb_md/gromacs/grompp.cwl
    in:
      config: step8_gppmin_config
      input_gro_path: step7_genion/output_gro_file
      input_top_zip_path: step7_genion/output_top_zip_file
    out: [output_tpr_file]

  step9_mdrun_min:
    label: Energetically Minimize the System - part 2
    run: biobb/biobb_adapters/cwl/biobb_md/gromacs/mdrun.cwl
    in:
      input_tpr_path: step8_grompp_min/output_tpr_file
    out: [output_trr_file, output_gro_file, output_edr_file, output_log_file]

  step10_energy_min:
    label: Energetically Minimize the System - part 3
    run: biobb/biobb_adapters/cwl/biobb_analysis/gromacs/gmx_energy.cwl
    in:
      config: step10_energy_min_config
      output_xvg_path: step10_energy_min_name
      input_energy_path: step9_mdrun_min/output_edr_file
    out: [output_xvg_file]

  step11_grompp_nvt:
    label: Equilibrate the System (NVT) - part 1
    run: biobb/biobb_adapters/cwl/biobb_md/gromacs/grompp.cwl
    in:
      config: step11_gppnvt_config
      input_gro_path: step9_mdrun_min/output_gro_file
      input_top_zip_path: step7_genion/output_top_zip_file
    out: [output_tpr_file]

  step12_mdrun_nvt:
    label: Equilibrate the System (NVT) - part 2
    run: biobb/biobb_adapters/cwl/biobb_md/gromacs/mdrun.cwl
    in:
      input_tpr_path: step11_grompp_nvt/output_tpr_file
    out: [output_trr_file, output_gro_file, output_edr_file, output_log_file, output_cpt_file]

  step13_energy_nvt:
    label: Equilibrate the System (NVT) - part 3
    run: biobb/biobb_adapters/cwl/biobb_analysis/gromacs/gmx_energy.cwl
    in:
      config: step13_energy_nvt_config
      output_xvg_path: step13_energy_nvt_name
      input_energy_path: step12_mdrun_nvt/output_edr_file
    out: [output_xvg_file]

  step14_grompp_npt:
    label: Equilibrate the System (NPT) - part 1
    run: biobb/biobb_adapters/cwl/biobb_md/gromacs/grompp.cwl
    in:
      config: step14_gppnpt_config
      input_gro_path: step12_mdrun_nvt/output_gro_file
      input_top_zip_path: step7_genion/output_top_zip_file
      input_cpt_path:  step12_mdrun_nvt/output_cpt_file
    out: [output_tpr_file]

  step15_mdrun_npt:
    label: Equilibrate the System (NPT) - part 2
    run: biobb/biobb_adapters/cwl/biobb_md/gromacs/mdrun.cwl
    in:
      input_tpr_path: step14_grompp_npt/output_tpr_file
    out: [output_trr_file, output_gro_file, output_edr_file, output_log_file, output_cpt_file]

  step16_energy_npt:
    label: Equilibrate the System (NPT) - part 3
    run: biobb/biobb_adapters/cwl/biobb_analysis/gromacs/gmx_energy.cwl
    in:
      config: step16_energy_npt_config
      output_xvg_path: step16_energy_npt_name
      input_energy_path: step15_mdrun_npt/output_edr_file
    out: [output_xvg_file]

  step17_grompp_md:
    label: Free Molecular Dynamics Simulation - part 1
    run: biobb/biobb_adapters/cwl/biobb_md/gromacs/grompp.cwl
    in:
      config: step17_gppmd_config
      input_gro_path: step15_mdrun_npt/output_gro_file
      input_top_zip_path: step7_genion/output_top_zip_file
      input_cpt_path:  step15_mdrun_npt/output_cpt_file
    out: [output_tpr_file]

  step18_mdrun_md:
    label: Free Molecular Dynamics Simulation - part 2
    run: biobb/biobb_adapters/cwl/biobb_md/gromacs/mdrun.cwl
    in:
      input_tpr_path: step17_grompp_md/output_tpr_file
    out: [output_trr_file, output_gro_file, output_edr_file, output_log_file, output_cpt_file]

  step19_rmsfirst:
    label: Post-processing Resulting 3D Trajectory - part 1
    run: biobb/biobb_adapters/cwl/biobb_analysis/gromacs/gmx_rms.cwl
    in:
      config: step19_rmsfirst_config
      output_xvg_path: step19_rmsfirst_name
      input_structure_path: step17_grompp_md/output_tpr_file
      input_traj_path: step18_mdrun_md/output_trr_file
    out: [output_xvg_file]

  step20_rmsexp:
    label: Post-processing Resulting 3D Trajectory - part 2
    run: biobb/biobb_adapters/cwl/biobb_analysis/gromacs/gmx_rms.cwl
    in:
      config: step20_rmsexp_config
      output_xvg_path: step20_rmsexp_name
      input_structure_path: step8_grompp_min/output_tpr_file
      input_traj_path: step18_mdrun_md/output_trr_file
    out: [output_xvg_file]

  step21_rgyr:
    label: Post-processing Resulting 3D Trajectory - part 3
    run: biobb/biobb_adapters/cwl/biobb_analysis/gromacs/gmx_rgyr.cwl
    in:
      config: step21_rgyr_config
      input_structure_path: step8_grompp_min/output_tpr_file
      input_traj_path: step18_mdrun_md/output_trr_file
    out: [output_xvg_file]

  step22_image:
    label: Post-processing Resulting 3D Trajectory - part 4
    run: biobb/biobb_adapters/cwl/biobb_analysis/gromacs/gmx_image.cwl
    in:
      config: step22_image_config
      input_top_path: step17_grompp_md/output_tpr_file
      input_traj_path: step18_mdrun_md/output_trr_file
    out: [output_traj_file]

  step23_dry:
    label: Post-processing Resulting 3D Trajectory - part 5
    run: biobb/biobb_adapters/cwl/biobb_analysis/gromacs/gmx_trjconv_str.cwl
    in:
      config: step23_dry_config
      input_structure_path: step18_mdrun_md/output_gro_file
      input_top_path: step17_grompp_md/output_tpr_file
    out: [output_str_file]

Inputs:

All inputs for the BioExcel building blocks are defined as strings. Not all the steps in this particular example need external inputs, some of them just works using as input/s an output (or outputs) from previous steps (e.g. step2_fixsidechain). For the steps that need input, all of them will receive a JSON formatted input (of type string), with the properties parameters of the building blocks (config). Apart from that, some of the building blocks in this example are receiving two different input parameters: the properties (e.g. step1_pdb_config) and the name of the output file to be written (e.g. step1_pdb_name). This is particularly useful to identify the files generated by different steps of the workflow. Besides, in cases where the same building block is used more than once, using the default value for the output files will cause the overwritting of the results generated by previous steps (e.g. energy calculation steps).

All these inputs will be filled up with values from the separated YAML input file.

In [ ]:
inputs:
  step1_pdb_name: string
  step1_pdb_config: string
  step4_editconf_config: string
  step6_gppion_config: string
  step7_genion_config: string
  step8_gppmin_config: string
  step10_energy_min_config: string
  step10_energy_min_name: string
  step11_gppnvt_config: string
  step13_energy_nvt_config: string
  step13_energy_nvt_name: string
  step14_gppnpt_config: string
  step16_energy_npt_config: string
  step16_energy_npt_name: string
  step17_gppmd_config: string
  step19_rmsfirst_config: string
  step19_rmsfirst_name: string
  step20_rmsexp_config: string
  step20_rmsexp_name: string
  step21_rgyr_config: string
  step22_image_config: string
  step23_dry_config: string

Outputs:

The outputs section contains the set of final outputs from the workflow. In this case, outputs from different steps of the workflow are considered final outputs:

  • Trajectories:
    • trr: Raw trajectory from the free simulation step.
    • trr_imaged_dry: Post-processed trajectory, dehydrated, imaged (rotations and translations removed) and centered.
  • Structures:
    • gro: Raw structure from the free simulation step.
    • gro_dry: Resulting protein structure taken from the post-processed trajectory, to be used as a topology, usually for visualization purposes.
  • Topologies:
    • tpr: GROMACS portable binary run input file, containing the starting structure of the simulation, the molecular topology and all the simulation parameters.
    • top: GROMACS topology file, containing the molecular topology in an ASCII readable format.
  • System Setup Observables:
    • xvg_min: Potential energy of the system during the minimization step.
    • xvg_nvt: Temperature of the system during the NVT equilibration step.
    • xvg_npt: Pressure and density of the system (box) during the NPT equilibration step.
  • Simulation Analysis:
    • xvg_rmsfirst: Root Mean Square deviation (RMSd) throughout the whole free simulation step against the first snapshot of the trajectory (equilibrated system).
    • xvg_rmsexp: Root Mean Square deviation (RMSd) throughout the whole free simulation step against the experimental structure (minimized system).
    • xvg_rgyr: Radius of Gyration (RGyr) of the molecule throughout the whole free simulation step.
  • Checkpoint file:
    • cpt: GROMACS portable checkpoint file, allowing to restore (continue) the simulation from the last step of the setup process.

Please note that the name of the output files is sometimes fixed by a specific input (e.g. step10_energy_min_name), whereas when no specific name is given as input, the default value is used (e.g. system.tpr). Default values can be found in the CWL description files for each building block (biobb_adapters).

In [ ]:
outputs:
  trr:
    label: Trajectories - Raw trajectory
    doc: |
      Raw trajectory from the free simulation step
    type: File
    outputSource: step18_mdrun_md/output_trr_file
    
  trr_imaged_dry:
    label: Trajectories - Post-processed trajectory
    doc: |
      Post-processed trajectory, dehydrated, imaged (rotations and translations
      removed) and centered.
    type: File
    outputSource: step22_image/output_traj_file
    
  gro_dry:
    label: Resulting protein structure
    doc: |
      Resulting protein structure taken from the post-processed trajectory, to
      be used as a topology, usually for visualization purposes.
    type: File
    outputSource: step23_dry/output_str_file
    
  gro:
    label: Structures - Raw structure
    doc: |
      Raw structure from the free simulation step.
    type: File
    outputSource: step18_mdrun_md/output_gro_file

  cpt:
    label: Checkpoint file
    doc: |
      GROMACS portable checkpoint file, allowing to restore (continue) the
      simulation from the last step of the setup process.
    type: File
    outputSource: step18_mdrun_md/output_cpt_file

  tpr:
    label: Topologies GROMACS portable binary run
    doc: |
      GROMACS portable binary run input file, containing the starting structure
      of the simulation, the molecular topology and all the simulation parameters.
    type: File
    outputSource: step17_grompp_md/output_tpr_file

  top:
    label: GROMACS topology file
    doc: |
      GROMACS topology file, containing the molecular topology in an ASCII
      readable format.
    type: File
    outputSource: step7_genion/output_top_zip_file
    
  xvg_min:
    label: System Setup Observables - Potential Energy
    doc: |
      Potential energy of the system during the minimization step.
    type: File
    outputSource: step10_energy_min/output_xvg_file

  xvg_nvt:
    label: System Setup Observables - Temperature
    doc: |
      Temperature of the system during the NVT equilibration step.
    type: File
    outputSource: step13_energy_nvt/output_xvg_file
    
  xvg_npt:
    label: System Setup Observables - Pressure and density 
    type: File
    outputSource: step16_energy_npt/output_xvg_file
    
  xvg_rmsfirst:
    label: Simulation Analysis
    doc: |
      Root Mean Square deviation (RMSd) throughout the whole free simulation
      step against the first snapshot of the trajectory (equilibrated system).
    type: File
    outputSource: step19_rmsfirst/output_xvg_file
  xvg_rmsexp:
    label: Simulation Analysis
    doc: |
      Root Mean Square deviation (RMSd) throughout the whole free simulation
      step against the experimental structure (minimized system).
    type: File
    outputSource: step20_rmsexp/output_xvg_file
    
  xvg_rgyr:
    label: Simulation Analysis
    doc: |
      Radius of Gyration (RGyr) of the molecule throughout the whole free simulation step
    type: File
    outputSource: step21_rgyr/output_xvg_file

Complete workflow:

The complete CWL described workflow to run a Molecular Dynamics Setup on a protein structure can be found in the next cell. The representation of the workflow using the CWL Viewer web service can be found here: XXXXXX. The full workflow is a combination of the inputs, outputs and steps revised in the previous cells.

In [ ]:
# Protein MD-Setup CWL workflow with BioExcel building blocks
# https://github.com/bioexcel/biobb_wf_md_setup

#!/usr/bin/env cwl-runner

cwlVersion: v1.0
class: Workflow
inputs:
  step1_pdb_name: string
  step1_pdb_config: string
  step4_editconf_config: string
  step6_gppion_config: string
  step7_genion_config: string
  step8_gppmin_config: string
  step10_energy_min_config: string
  step10_energy_min_name: string
  step11_gppnvt_config: string
  step13_energy_nvt_config: string
  step13_energy_nvt_name: string
  step14_gppnpt_config: string
  step16_energy_npt_config: string
  step16_energy_npt_name: string
  step17_gppmd_config: string
  step19_rmsfirst_config: string
  step19_rmsfirst_name: string
  step20_rmsexp_config: string
  step20_rmsexp_name: string
  step21_rgyr_config: string
  step22_image_config: string
  step23_dry_config: string

outputs:
  trr:
    label: Trajectories - Raw trajectory
    doc: |
      Raw trajectory from the free simulation step
    type: File
    outputSource: step18_mdrun_md/output_trr_file
    
  trr_imaged_dry:
    label: Trajectories - Post-processed trajectory
    doc: |
      Post-processed trajectory, dehydrated, imaged (rotations and translations
      removed) and centered.
    type: File
    outputSource: step22_image/output_traj_file
    
  gro_dry:
    label: Resulting protein structure
    doc: |
      Resulting protein structure taken from the post-processed trajectory, to
      be used as a topology, usually for visualization purposes.
    type: File
    outputSource: step23_dry/output_str_file
    
  gro:
    label: Structures - Raw structure
    doc: |
      Raw structure from the free simulation step.
    type: File
    outputSource: step18_mdrun_md/output_gro_file

  cpt:
    label: Checkpoint file
    doc: |
      GROMACS portable checkpoint file, allowing to restore (continue) the
      simulation from the last step of the setup process.
    type: File
    outputSource: step18_mdrun_md/output_cpt_file

  tpr:
    label: Topologies GROMACS portable binary run
    doc: |
      GROMACS portable binary run input file, containing the starting structure
      of the simulation, the molecular topology and all the simulation parameters.
    type: File
    outputSource: step17_grompp_md/output_tpr_file

  top:
    label: GROMACS topology file
    doc: |
      GROMACS topology file, containing the molecular topology in an ASCII
      readable format.
    type: File
    outputSource: step7_genion/output_top_zip_file
    
  xvg_min:
    label: System Setup Observables - Potential Energy
    doc: |
      Potential energy of the system during the minimization step.
    type: File
    outputSource: step10_energy_min/output_xvg_file

  xvg_nvt:
    label: System Setup Observables - Temperature
    doc: |
      Temperature of the system during the NVT equilibration step.
    type: File
    outputSource: step13_energy_nvt/output_xvg_file
    
  xvg_npt:
    label: System Setup Observables - Pressure and density 
    type: File
    outputSource: step16_energy_npt/output_xvg_file
    
  xvg_rmsfirst:
    label: Simulation Analysis
    doc: |
      Root Mean Square deviation (RMSd) throughout the whole free simulation
      step against the first snapshot of the trajectory (equilibrated system).
    type: File
    outputSource: step19_rmsfirst/output_xvg_file
  xvg_rmsexp:
    label: Simulation Analysis
    doc: |
      Root Mean Square deviation (RMSd) throughout the whole free simulation
      step against the experimental structure (minimized system).
    type: File
    outputSource: step20_rmsexp/output_xvg_file
    
  xvg_rgyr:
    label: Simulation Analysis
    doc: |
      Radius of Gyration (RGyr) of the molecule throughout the whole free simulation step
    type: File
    outputSource: step21_rgyr/output_xvg_file

steps:
  step1_pdb:
    label: Fetch PDB Structure
    doc: |
      Download a protein structure from the PDB database
    run: biobb/biobb_adapters/cwl/biobb_io/mmb_api/pdb.cwl
    in:
      output_pdb_path: step1_pdb_name
      config: step1_pdb_config
    out: [output_pdb_file]

  step2_fixsidechain:
    label: Fix Protein structure
    doc: |
      Fix the side chains, adding any side chain atoms missing in the
      original structure.
    run: biobb/biobb_adapters/cwl/biobb_model/model/fix_side_chain.cwl
    in:
      input_pdb_path: step1_pdb/output_pdb_file
    out: [output_pdb_file]

  step3_pdb2gmx:
    label: Create Protein System Topology
    run: biobb/biobb_adapters/cwl/biobb_md/gromacs/pdb2gmx.cwl
    in:
      input_pdb_path: step2_fixsidechain/output_pdb_file
    out: [output_gro_file, output_top_zip_file]

  step4_editconf:
    label: Create Solvent Box
    run: biobb/biobb_adapters/cwl/biobb_md/gromacs/editconf.cwl
    in:
      input_gro_path: step3_pdb2gmx/output_gro_file
    out: [output_gro_file]

  step5_solvate:
    label: Fill the Box with Water Molecules
    run: biobb/biobb_adapters/cwl/biobb_md/gromacs/solvate.cwl
    in:
      input_solute_gro_path: step4_editconf/output_gro_file
      input_top_zip_path: step3_pdb2gmx/output_top_zip_file
    out: [output_gro_file, output_top_zip_file]

  step6_grompp_genion:
    label: Add Ions - part 1
    run: biobb/biobb_adapters/cwl/biobb_md/gromacs/grompp.cwl
    in:
      config: step6_gppion_config
      input_gro_path: step5_solvate/output_gro_file
      input_top_zip_path: step5_solvate/output_top_zip_file
    out: [output_tpr_file]

  step7_genion:
    label: Add Ions - part 2
    run: biobb/biobb_adapters/cwl/biobb_md/gromacs/genion.cwl
    in:
      config: step7_genion_config
      input_tpr_path: step6_grompp_genion/output_tpr_file
      input_top_zip_path: step5_solvate/output_top_zip_file
    out: [output_gro_file, output_top_zip_file]

  step8_grompp_min:
    label: Energetically Minimize the System - part 1
    run: biobb/biobb_adapters/cwl/biobb_md/gromacs/grompp.cwl
    in:
      config: step8_gppmin_config
      input_gro_path: step7_genion/output_gro_file
      input_top_zip_path: step7_genion/output_top_zip_file
    out: [output_tpr_file]

  step9_mdrun_min:
    label: Energetically Minimize the System - part 2
    run: biobb/biobb_adapters/cwl/biobb_md/gromacs/mdrun.cwl
    in:
      input_tpr_path: step8_grompp_min/output_tpr_file
    out: [output_trr_file, output_gro_file, output_edr_file, output_log_file]

  step10_energy_min:
    label: Energetically Minimize the System - part 3
    run: biobb/biobb_adapters/cwl/biobb_analysis/gromacs/gmx_energy.cwl
    in:
      config: step10_energy_min_config
      output_xvg_path: step10_energy_min_name
      input_energy_path: step9_mdrun_min/output_edr_file
    out: [output_xvg_file]

  step11_grompp_nvt:
    label: Equilibrate the System (NVT) - part 1
    run: biobb/biobb_adapters/cwl/biobb_md/gromacs/grompp.cwl
    in:
      config: step11_gppnvt_config
      input_gro_path: step9_mdrun_min/output_gro_file
      input_top_zip_path: step7_genion/output_top_zip_file
    out: [output_tpr_file]

  step12_mdrun_nvt:
    label: Equilibrate the System (NVT) - part 2
    run: biobb/biobb_adapters/cwl/biobb_md/gromacs/mdrun.cwl
    in:
      input_tpr_path: step11_grompp_nvt/output_tpr_file
    out: [output_trr_file, output_gro_file, output_edr_file, output_log_file, output_cpt_file]

  step13_energy_nvt:
    label: Equilibrate the System (NVT) - part 3
    run: biobb/biobb_adapters/cwl/biobb_analysis/gromacs/gmx_energy.cwl
    in:
      config: step13_energy_nvt_config
      output_xvg_path: step13_energy_nvt_name
      input_energy_path: step12_mdrun_nvt/output_edr_file
    out: [output_xvg_file]

  step14_grompp_npt:
    label: Equilibrate the System (NPT) - part 1
    run: biobb/biobb_adapters/cwl/biobb_md/gromacs/grompp.cwl
    in:
      config: step14_gppnpt_config
      input_gro_path: step12_mdrun_nvt/output_gro_file
      input_top_zip_path: step7_genion/output_top_zip_file
      input_cpt_path:  step12_mdrun_nvt/output_cpt_file
    out: [output_tpr_file]

  step15_mdrun_npt:
    label: Equilibrate the System (NPT) - part 2
    run: biobb/biobb_adapters/cwl/biobb_md/gromacs/mdrun.cwl
    in:
      input_tpr_path: step14_grompp_npt/output_tpr_file
    out: [output_trr_file, output_gro_file, output_edr_file, output_log_file, output_cpt_file]

  step16_energy_npt:
    label: Equilibrate the System (NPT) - part 3
    run: biobb/biobb_adapters/cwl/biobb_analysis/gromacs/gmx_energy.cwl
    in:
      config: step16_energy_npt_config
      output_xvg_path: step16_energy_npt_name
      input_energy_path: step15_mdrun_npt/output_edr_file
    out: [output_xvg_file]

  step17_grompp_md:
    label: Free Molecular Dynamics Simulation - part 1
    run: biobb/biobb_adapters/cwl/biobb_md/gromacs/grompp.cwl
    in:
      config: step17_gppmd_config
      input_gro_path: step15_mdrun_npt/output_gro_file
      input_top_zip_path: step7_genion/output_top_zip_file
      input_cpt_path:  step15_mdrun_npt/output_cpt_file
    out: [output_tpr_file]

  step18_mdrun_md:
    label: Free Molecular Dynamics Simulation - part 2
    run: biobb/biobb_adapters/cwl/biobb_md/gromacs/mdrun.cwl
    in:
      input_tpr_path: step17_grompp_md/output_tpr_file
    out: [output_trr_file, output_gro_file, output_edr_file, output_log_file, output_cpt_file]

  step19_rmsfirst:
    label: Post-processing Resulting 3D Trajectory - part 1
    run: biobb/biobb_adapters/cwl/biobb_analysis/gromacs/gmx_rms.cwl
    in:
      config: step19_rmsfirst_config
      output_xvg_path: step19_rmsfirst_name
      input_structure_path: step17_grompp_md/output_tpr_file
      input_traj_path: step18_mdrun_md/output_trr_file
    out: [output_xvg_file]

  step20_rmsexp:
    label: Post-processing Resulting 3D Trajectory - part 2
    run: biobb/biobb_adapters/cwl/biobb_analysis/gromacs/gmx_rms.cwl
    in:
      config: step20_rmsexp_config
      output_xvg_path: step20_rmsexp_name
      input_structure_path: step8_grompp_min/output_tpr_file
      input_traj_path: step18_mdrun_md/output_trr_file
    out: [output_xvg_file]

  step21_rgyr:
    label: Post-processing Resulting 3D Trajectory - part 3
    run: biobb/biobb_adapters/cwl/biobb_analysis/gromacs/gmx_rgyr.cwl
    in:
      config: step21_rgyr_config
      input_structure_path: step8_grompp_min/output_tpr_file
      input_traj_path: step18_mdrun_md/output_trr_file
    out: [output_xvg_file]

  step22_image:
    label: Post-processing Resulting 3D Trajectory - part 4
    run: biobb/biobb_adapters/cwl/biobb_analysis/gromacs/gmx_image.cwl
    in:
      config: step22_image_config
      input_top_path: step17_grompp_md/output_tpr_file
      input_traj_path: step18_mdrun_md/output_trr_file
    out: [output_traj_file]

  step23_dry:
    label: Post-processing Resulting 3D Trajectory - part 5
    run: biobb/biobb_adapters/cwl/biobb_analysis/gromacs/gmx_trjconv_str.cwl
    in:
      config: step23_dry_config
      input_structure_path: step18_mdrun_md/output_gro_file
      input_top_path: step17_grompp_md/output_tpr_file
    out: [output_str_file]

Input of the run:

As previously stated, all CWL workflows are divided in two files: the CWL description and the YAML or JSON files containing all workflow inputs. The following cell presents the YAML file describing the inputs of the run for the Protein Gromacs MD Setup workflow.

All the steps were defined as strings in the CWL workflow; Building blocks inputs ending by "_name" contain a simple string with the wanted file name; Building blocks inputs ending by "_config" contain the properties parameters in a string reproducing a JSON format. Please note here that all double quotes in JSON format must be escaped. The properties parameters were taken from the original Protein Gromacs MD Setup workflow Jupyter Notebook tutorial. Please refer to it to find information about the values used.

In [ ]:
# Protein MD-Setup CWL workflow with BioExcel building blocks - Input YAML configuration file
# https://github.com/bioexcel/biobb_wf_md_setup

step1_pdb_name: 'tutorial.pdb'
step1_pdb_config: '{"pdb_code" : "1aki"}'
step4_editconf_config: '{"box_type": "cubic","distance_to_molecule": 1.0}'
step6_gppion_config: '{"mdp": {"type":"minimization"}}'
step7_genion_config: '{"neutral": "True"}'
step8_gppmin_config: '{"mdp": {"type":"minimization", "nsteps":"5000", "emtol":"500"}}'
step10_energy_min_config: '{"terms":  ["Potential"]}'
step10_energy_min_name: 'energy_min.xvg'
step11_gppnvt_config: '{"mdp": {"type":"nvt", "nsteps":"5000", "dt":0.002, "define":"-DPOSRES"}}'
step13_energy_nvt_config: '{"terms":  ["Temperature"]}'
step13_energy_nvt_name: 'energy_nvt.xvg'
step14_gppnpt_config: '{"mdp": {"type":"npt", "nsteps":"5000"}}'
step16_energy_npt_config: '{"terms":  ["Pressure","Density"]}'
step16_energy_npt_name: 'energy_npt.xvg'
step17_gppmd_config: '{"mdp": {"type":"free", "nsteps":"50000"}}'
step19_rmsfirst_config: '{"selection": "Backbone"}'
step19_rmsfirst_name: 'rmsd_first.xvg'
step20_rmsexp_config: '{"selection": "Backbone"}'
step20_rmsexp_name: 'rmsd_exp.xvg'
step21_rgyr_config: '{"selection": "Backbone"}'
step22_image_config: '{"center_selection":"Protein","output_selection":"Protein","pbc":"mol"}'
step23_dry_config: '{"selection": "Protein"}'

Running the CWL workflow:

The final step of the process is running the workflow described in CWL. For that, the complete workflow description should be written to a file (e.g. BioExcel-CWL-MDSetup.cwl), the YAML input should be written to a separate file (e.g. BioExcel-CWL-MDSetup-job.yml) and finally both files should be used with the CWL tool description reference implementation executer (cwltool).

As in the previous example, it is important to note that in order to properly run the CWL workflow, the CWL descriptions for all the building blocks used in the workflow should be accessible from the file system. In this example, all the CWL descriptions needed where downloaded from the BioExcel building blocks adapters github repository to a folder named biobb_adapters.

It is worth to note that as this workflow is using different BioExcel building block modules (biobb_io, biobb_model, biobb_md and biobb_analysis), so the Docker container for each of the modules will be downloaded the first time that it is launched. This process could take some time (and disk space). Once all the Docker containers are correctly downloaded and integrated in the system, the workflow should take around 1h (depending on the machine used).

The command line is shown in the cell below:

In [ ]:
# Run CWL workflow with CWL tool description reference implementation (cwltool).
cwltool BioExcel-CWL-MDSetup.cwl BioExcel-CWL-MDSetup-job.yml

Questions & Comments

Questions, issues, suggestions and comments are really welcome!

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