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caArray Training Overview
Introductions Brief History of caArray Workflow and Operating Procedures caArray Product Overview Questions and Answers
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Introductions
Who are you? What do you know about caArray? How will you be using caArray? What is one thing you would like to learn a about
caArray?
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caArray…The History
Need for standardization Need for Compliance caArray is
– caBig Compliant– MIAME Compliant– MAGE Compliant
caArray is approved for data submission and publication
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caArray…Workflow Step-by-Step
Create User Account– Establishes what access permissions you are granted
Complete Contacts Complete Protocols Complete Array Designs Complete Ontologies (controlled vocabularies) Complete Biomaterials (sample information) Submit Experiments
– Add Hybridizations Upload Experiments Add or Modify Experiments Publish Data Lock Final Data
caArray Workflow - Diagram
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User Accounts
Establishes Access Permissions– Public– Private– Consortium
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Logging In
Type Login ID Type Password
– If you forget your Username and Password contact NCICB Application Support at
888-478-4423 301-451-4384 [email protected]
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Contacts Order of Operations
Verify that a contact exists by using the Search options– Search Either Organization or People
If contact does not exist – Add New Person, New Organization or both
If adding a New Person contact verify the Organization in which the person is affiliated exists– If the Organization does not exist add the New
Organization first before adding the New Person as a person is REQUIRED to be affiliated with an organization
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Search Organization
Can use Wildcards
– NCI*– *Cancer*
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Adding a New Organization
If the organization does not exist
– Add the New Organization
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Adding the New Organization Information
Complete the required fields
– Required fields are indicated by *
Submit the New Organization
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Search People
Can use wildcards for either first or last name
– First Name: Jamie– Last Name: *
– First Name: *– Last Name: Keller
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Adding a New Person
Add yourself as a contact
– Select New Person– Complete the required
fields Required fields are
indicated by an *– When completed,
select Submit to add yourself as a Contact
NOTE: If you do not see your organization on the list of options you MUST add your organization
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Modifying a Contact
Occasionally changes or updates may need to be made to either the Organization or Person (e.g. an area code has changed)
– Search People or Search Organization
– Select Modify
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Modifying a Contact continued…
Make all necessary modifications
– Remember to save any modifications
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Protocols
Steps taken in a Microarray procedure– It is a “recipe” of items used to create the procedure– Well written and documented Protocols can be reused
Affymetrix Labeling and Hybridization Protocol GenePix Scanning Protocol
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Two Types of Protocols
Wet Lab Protocols– Hybridization Protocol– Labeling Protocol
Dry Lab Protocols– Image Acquisition
GenePix
– Feature Extraction Affymetrix GCOS
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Protocols Order of Operations
Verify Protocol exists– Search Protocols
If Protocol does not exist– Verify Hardware exists…for Dry Lab Only
Search Hardware If Hardware does not exist
– Add Hardware
– Verify Software exists…For Dry Lab Only Search Software If Software does not exist
– Add Software
Add New Protocol
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Creating a Dry Lab ProtocolMulti-Step Approach
1. Verify Protocol does not already exist: Search Protocol
2. Verify Hardware used in the Dry Lab Protocol exist: Search Hardware
A. If Hardware does NOT exist: Add Hardware
3. Verify the Software used in the Dry Lab Protocol exists: Search Software
A. If the Software does NOT exist: Add Software
4. Once the above steps are completed: New Protocol
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Verify Protocol ExistsSTEP 1 -- Search Protocol
Can Search by:
– Type---Best way to search The Kind of Protocol
– Array_ Manufacturing_ Protocol
– Name Any name given to a
created protocol– Dr. Moliuex RNA
Labeling Protocol
– Visibility Who can view the protocol
– Public
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Creating A Dry Lab ProtocolSTEP 2 -- Searching Hardware
Verify Hardware exists– Search Hardware
Hardware Type– Type of Hardware
used in Protocol• Array_Scanner
Hardware Manufacturer
– Who makes the equipment
• Affymetrix Hardware Model Visibility
– Who can view the Hardware
• Public
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Creating a Dry Lab ProtocolSTEP 2A -- New Hardware
Select New Hardware– Name
Equipment in the lab– Axon Scanner
– Model• Whatever model
number is associated with the equipment
– GenePix 4000b
– Type• What kind of
equipment is it– Array_Scanner
– Manufacturer• Who makes the
equipment– Axon Instruments
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Select New Hardware continued…
– URI (Uniform Resource Indicator also known as URL)
• The website of the Manufacturer
– http://www.moleculardevices.com
– Visibility• Who can utilize this
hardware for their protocols
– Public
Creating a Dry Lab ProtocolSTEP 2A -- New Hardware continued…
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Verify Software exists– Search Software
Software Type– Type of Software used
in Protocol• Array_Manufacture
_Software
Software Manufacturer– Who makes the
software• GenePix
Visibility– Who can utilize the
software in creating a protocol
• Public
Creating a Dry Lab Protocol STEP 3 -- Searching Software
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Select New Software– Name
Software in the lab– Generic Pro 4.0
– Type• What kind of software it
is– Array_Manufacture_
Software
– Manufacturer• Who makes the software
– Generic
Creating a Dry Lab ProtocolSTEP 3A -- New Software
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Adding New Software continued…
– URI (Uniform Resource Indicator also known as URL)
• The website of the Software Manufacturer
– http://www.axon.com /GN_GenePixSoftware.html
– Visibility• Who can utilize this
software in creating protocols
– Public
Creating a Dry Lab ProtocolSTEP 3A -- New Software continued…
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Adding a Dry Lab ProtocolSTEP 4 -- New Protocol
New Protocol– Name
The name of the new Protocol
– Affymetrix Eukaryotic Sample and Array Processing Protocol
– Type The protocol type
– Array_Manufacturing_Protocol
– Specify New Type The protocol type
– Option that does not already exist in the Type drop down list
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New Protocol continued…– URI (Uniform Resource Indicator
also known as URL) The website of the
Organization submitting the Protocol
– http://ncicb.nci.nih.gov
– Visibility Who can utilize this
software in creating protocols
– Public
• Select Submit to continue adding a New Protocol
Adding a Dry Lab ProtocolSTEP 4 -- New Protocol continued…
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Add Parameters (if applicable)
Add Hardware– The Hardware added in
Step 2A
Add Software– The Software added in
Step 3A
Adding a Dry Lab ProtocolSTEP 4 -- New Protocol continued…
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Creating a Wet Lab Protocola Two-Step Approach
1. Verify Protocol does not already exist: Search Protocol
2. Add: New Protocol
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Verify Protocol ExistsSTEP 1 -- Search Protocol
Can Search by:
– Type---Best way to search The Kind of Protocol
– Array_ Manufacturing_ Protocol
– Name Any Name given to a
created protocol– Dr. Moliuex RNA
Labeling Protocol
– Visibility Who can view the
Protocol– Public
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Adding A Wet Lab ProtocolSTEP 2 -- New Protocol
New Protocol– Name
The name of the new protocol
– RNA Processing
– Type The protocol type
– Grow
– Specify New Type The protocol type
– Option that does not already exist in the Type Drop Down List
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Adding A Wet Lab ProtocolSTEP 2 -- New Protocol continued…
New Protocol continued…– URI (Uniform Resource Indicator
also known as URL) The website of the
Organization submitting the Protocol
http://ncicb.nci.nih.gov
– Visibility Who can utilize this
software in creating protocols
– Public
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Array Designs Descriptions of Microarrays that include
– Array Layout– Array Design– Type of technology – Substrate– Surface– Attachment– Strand Type
Gives users ability to add and search record Allows for replication Good Array Designs can be reused in future
experiments
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Array DesignOrder of Operations
Verify that the Array exists– If the Array Does not Exist
Add Array...– New Array Design
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Search Array Design
You can Search By:– Technology Type –Best
way to Search What type of technology
is being used– In_situ_olgio_ features
– Array design name Name given by creator of
the array– NCICB Human1.119K
– Visibility Who can use and view
the array– Consortium
– Substrate Type What kind of material is
the array made of– Glass
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Searching continued…– Surface Type
What makes the probes stick to the slide
– Polylysine
– Attachment Type What is the mechanism
that makes the probes attach to the slide
– Ionic
– Organism What is the species from
which the array comes– Homo Sapiens
Search Array Design continued…
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Adding New Array Design
When adding New Array Design complete:
– Type Upload If you are using MAGE ML
you do not have to complete the the New Array Design Information Section
If you are using GenePix this is a GAL file
– Array Design Name What you are going to call
the array– Standard naming
convention for caArray is ORGANIZATION_SPICIES NAME_VERSION #_SPOTS ON ARRAY
• NCICB__Mus musculus_1.1_19K
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Adding a New Array Design continued…
New Array Design continued…
– Array Version The print number
– 1.1– Technology Type
The type of probe spotted/printed on the array
– cDNA– Substrate Type
Type of surface used for the array
– Glass– Surface Type
Type of material used to adhere array to the substrate
– Polylysine
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New Array Design continued…
– Attachment Type How the array is bonded to
the substrate and surface– Ionic
– Organism Species from which the
array is derived– Homo Sapiens
– Array Descriptor Short description of the
array– Can be copied and pasted
from outside sources– Max 4000 characters
– Visibility Who can use and view the
array– Consortium
Adding a New Array Designcontinued…
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Ontologies
Need for Common language– For example, BR CA to some this is brain cancer to other
this might be breast cancer…ontology makes it clear that breast cancer will always be referred to as Breast Cancer
Formal specification of the terms in a particular domain, and the relationship among those terms to one another. – The Microarray Gene Expression Data Society (MGED)
provides the ontology used by caArray.
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OntologiesOrder of Operations
Verify the existence of:– Cell Lines– Cell Types – Developmental Stages– Disease Stages– Disease States– Organism Parts– Strain or Line– Tumor Grading
If missing, add the above ontologies
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Ontologies
Search by:– Cell Line Name
Hela– Cell Types Name
Epithelial– Developmental Stage Name
Theiler Stage 3– Disease Stage Name
Dukes C Colon Cancer– Disease States Name
Lung Cancer– Organism Part Name
Colon– Strain or Line Name
Mouse Strain– Tumor Grading Name
Breast Cancer Stage 2
Search: Cell Lines, Cell Types, Developmental Stages, Disease Stages, Disease States, Organism Parts, Strain or Line, Tumor Grading
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Search continued…
– Public Databases NCI –Thesaurus ATCC Cultures
OntologiesSearch: Cell Lines, Cell Types, Developmental Stages, Disease Stages, Disease States, Organism Parts, Strain or Line, Tumor Grading continued…
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Add Ontologies:– Cell Line Name
Sm Cell Carcinoma 0312 (Lab identifier)
– Cell Type Name Epidermal
– Developmental Stage Name Embryo
– Disease Stage Name Stage 2
– Disease State Name Lung Cancer
– Organism Part Name Lung
– Strain or Line Name Mouse X
– Tumor Grading Name Grade 3
OntologiesAdd: Cell Lines, Cell Types, Developmental Stages, Disease Stages, Disease States, Organism Parts, Strain or Line, Tumor Grading
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Add Ontologies continued…
– Public Database (if applicable as private collections will not be found in public databases)
Private Cell_Ontology
– Accession Number If not part of a public
database, no accession number is needed
CL025681– URI (Uniform Resource Indicator
also known as URL)
• If not part of a public database, no URI is needed
– http://www.atcc.org
OntologiesAdd: Cell Lines, Cell Types, Developmental Stages, Disease Stages, Disease States, Organism Parts, Strain or Line, Tumor Grading continued…
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Biomaterials/Sample
Your samples that are materials of biological origin– Document all information on your samples
Biomaterials consist of: – Biosources
This is your sample prior to any treatment– Biopsy
• Lung Tumor Biopsy 1
– Biosamples The sample that resulted from treating the Biosource
– RNA extract• Lung Tumor RNA 1
– Labeled Extracts The labeled sample
– RNA Labeling• Lung Tumor 1 Cy5
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Biomaterials/Samples
BIOSOURCE
BIOSAMPLE
LABLED EXTRACT
Treatment = Biopsy (what was done to obtain the sample)
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BiomaterialsOrder of Operations
Search to verify the existence of:1. Biosource
2. Biosample related to Biosource
3. Labeled extracts related to Biosources If needed Submit/Add New:
1. Biosource
2. Biosamples related to the newly submitted Biosource
3. Labeled Extracts related to the newly submitted Biosources
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BiomaterialsSearch BioSources
Search by:– Biosource Type
The state of the material when received
– Fresh– Organism
Species from which the sample came
– Homo Sapiens– Visibility
Who can use and view the biomaterial
– Consortium– Biosource Name
The name of the Biosource– Lung Tumor 1
– Provider The name of the
organization or individual who provided the sample
– NIH Clinical Center
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BiomaterialsSearching Biosample
Search Biosamples by:– Sample Name
Name given to biosample– Lung Tumor RNA 1
– Biosource The name of the source
from which the sample is derived
– Lung Cancer Biopsy _1
– Organism Species from which the
sample came– Homo Sapiens
– Visibility Who can see the biosample
– Private
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Search Labeled Extracts by:
– Biosample The sample from which
the labeled extract is derived
– Lung_Cancer_1_RNA
– Organism Species from which the
sample came from– Homo Sapiens
– Visibility Who can see the labeled
extract– Private
BiomaterialsSearching Labeled Extracts
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BiomaterialsSubmit New Biosource
Submit New Biosource complete:
– Biosource Name What you want to call the
biosource– LungSamplePtX
– Description Short description of the
biosource including how it was obtained (4000 character max)
– Lung sample obtained from female patient age 65 with carcinoma using …
– Organism Species from which the
sample came from– Homo Sapiens
– Specify New Organism Type Utilized only if Species is not
on the drop down list in the Organism Field
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Submit New Biosource complete continued…
– Provider The name of the organization
or individual who provided the sample
– NIH Clinical Center– Biosource Type
The state of the material when received
– Fresh– Specify New Biosource Type
Utilized only if biosource is not on the drop down list in the Biosource Type field
– Visibility Who can see the Biosource
– Private Save
BiomaterialsSubmit New Biosource continued…
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BiomaterialsNew BioSample
Three Step Process
1. Identify the Biosource– If the biosource does not exist, it must be created prior
to adding the New Biosample
2. Identify the Treatment– The function performed on the biosource to create the
New Biosample
3. Identify the Protocol– If the Protocol does not exist, it must be created prior
to adding the New Biosample
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Biomaterials New Biosample
Step 1– Identify Biosource New Biosample – Step 1
Identify the Biosource:– Select Biosource
The biosource from which the sample is derived
– Lung_Cancer1– Name of Resulting
Biomaterial What you wish to name
the new biosample– Lung Cancer RNA 1
– Description of Resulting Biomaterial
A short description of how the biosample was derived
– Total RNA from Lung Tumor Biopsy
Select Next – Step 2 Identify Treatment
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New Biosample – Step 2 Identify Treatment :
– Applying a Protocol Protocols were created in
the Protocol tab and should be done prior to submitting biosamples
– Add New Treatment Event How the Biosource was
treated to create the Biosample
Treatment Type– Nucleic_Acid_Extraction
Biomaterials New Biosample
Step 2– Identify Treatment
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Biomaterials New Biosample
Step 2– Identify Treatment continued…
New Biosample – Step 2 Identify Treatment continued…
– Measurement The measurement of the
biosample– 5
– Unit Type The type of measurement used
– Mass Unit– Note that another field may
appear based on the Unit Type selected
• Unit• MG
Add Treatment Select Apply Protocol – Step 3
Identify Protocol
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New Biosample – Step 3 Apply Protocol:
– Applying a Protocol Protocols were created in
the Protocol tab and should be done prior to adding a New Biosample
– Activity Date– 10/10/04
– Performer– Who performed the
treatment (NOTE: This is a contacts added in the Contact tab if the name is missing it must be added in the Contacts tab prior to completing this section)
• Jane Liu Save
Biomaterials New Biosample
Step 3– Apply Protocol
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Biomaterials New Labeled Extract
Two Step Approach
Identify the treatment of the biosample which results in the New Labeled Extract– If the biosample does not exist, it must be created prior
to adding the New Labeled Extract Apply the Protocol
– If the Protocol does not exist, it must be created prior to adding the New Labeled Extract
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Biomaterials New Labeled Extract
Step 1– Identify Biosample Treatment New Labeled Extract –
Step 1 Identify the Biosample Treatment :
– Name of Resulting Extract The name of the extract
derived from the biosample– Lung_Tumor_1_Cy5
– Select a Biosample to be Labeled
This was created when the new biosample was added
– Lung_Cancer_RNA 1– Label
Detector– Biotin, Cy5
– Amount of Nucleic Acid Labeled
The numeric amount of nucleic acid
– 100
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New Labeled Extract – Step 1 Identify the Biosample Treatment continued…
– Unit of Mass The unit in which the acid is
measured– NG
– Material Type of Resulting Labeled Extract
Labeled Sample – Total RNA
– Visibility Who can use and view the
Labeled Extract– Consortium
Select Apply Protocol
Biomaterials New Labeled Extract
Step 1– Identify Biosample Treatment continued…
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New Labeled Extract – Step 2 Apply Protocol
– Applying a Protocol Protocols were created in
the Protocol tab and should be done prior to adding a New Labeled Extract
– Activity Date– 10/10/04
– Performer– Who performed the
treatment (NOTE: This is a contacts added in the Contact tab if the name is missing it must be added in the Contacts tab prior to completing this section)
• Jane Liu Save
Biomaterials New Labeled ExtractStep 2– Apply Protocol
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Submitting an Experiment
Complete Contacts Protocols Array Designs Ontologies Bio Materials
Submit Experiment
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Submit Experiment Order of Operations
Verify the Experiment has not been submitted– Search/Modify Experiments
Add New Experiment– Create Hybridizations– Determine Experimental Factors– Upload Experiment
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Search/Modify Experiment
You can Search/Modify Experiment by:– Experiment ID
Unique identification number
– 788918BK
– Experiment Name The name of the
experiment– JLK BLOOD 1.1
– Visibility Who can view the
Experiment– Consortium
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Search/Modify Experiment continued…
You can Search By continued…
– Experiment Type What kind of experiment
are you looking for– RNA_Stability Design
– Principal Investigator Who created the
experiment– Dr. John Maiti
– Organism Species from which the
experiment was derived– Mus Musculus
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Import MAGE ML File
MAGE files can be imported as part of the experiment documentation
To Import MAGE ML:– File Name
To locate the MAGE file to be imported Browse to find the file
– Message to Curator A short message to the
data curator regarding the MAGE file, documenting from where the MAGE file came, etc
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ExperimentNew Experiment
Multi-Step Approach1. General Experiment Information2. Experimental Factors3. Publications
– Any Publications that are part of the experiment4. Quality Control Steps
– Measures taken to ensure
5. Additional Qualifiers6. Additional Upload Files7. MAGE ML Download8. Hybridizations
– Protocols 1. Image Acquisition – Dry Lab Protocols2. Feature Extractions – Wet Lab Protocols
9. Upload Hybridization – Submit Experiment
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ExperimentNew Experiment
Step 1 – General Experiment Information New Experiment – Step 1
General Experiment Information
– Title The name of the
experiment– Lung cancer
experimental factors
– Experiment completion date The day the experiment
was completed– 05/25/03
– Experiment design Type High level description of
the kind of experimental design being utilized
– Dose Response
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ExperimentNew Experiment
Step 1 – General Experiment Information continued…
New Experiment – Step 1 General Experiment Information continued…:
– Visibility Who can view, or use the
Experiment– Consortium
– Description A description of the
experiment (max 4000 characters)
– Your white paper for the experiment
– Principal Investigator Who is responsible for the
Experiment (This list comes from the Contacts tab, if the contact is missing you must return to the Contacts tab and enter the New Contact)
– Dr. John Maiti
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New Experiment – Step 1 General Experiment Information continued…
– Contact Person The person to contact if
more information is needed (This list comes from the Contacts tab, if the contact is missing you must return to the contacts tab and enter the New Contact)
– Jamie Keller– Number of Experimental
Factors Parameters of a study that
influence the experimental result
– 2 Next – Step 2 Experimental
Factors
ExperimentNew Experiment
Step 1 – General Experiment Information continued…
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ExperimentNew Experiment
Step 2 – Experimental Factors
New Experiment – Step 2 Experimental Factors
– Factor Name The type of experimental
factors used– Dose
– Factor Type How the experimental
factor is classified– Labeling Protocol
– Scale How the factor is measured
– Linear_Scale– Levels
The amount of factor given– 25 mcg
Next – Step 3 Experimental Factors
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New Experiment – Step 3 Additional Publications
– Add A New Publication if applicable
Any additional supporting publications used or referenced in the experiment
ExperimentNew Experiment
Step 3 – Additional Publications
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ExperimentNew Experiment
Step 4 – Quality Control
New Experiment – Step 4 Quality Control
– Add Quality Control Steps if applicable
Any quality assurance measures taken with the experiment
– Peer Review
– Reverse Fluoresces
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ExperimentNew Experiment
Step 5 – Additional Qualifiers
New Experiment – Step 5 Additional Qualifiers
– Add Additional Qualifiers if applicable
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ExperimentNew Experiment
Step 6 – Additional Upload Files
New Experiment – Step 6 Additional Upload Files
– Add Additional Upload Files if applicable
Any additional materials used in conducting the experiment
– Image File
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ExperimentNew Experiment
Step 7 – Hybridizations
New Experiment – Step 7 Hybridizations
– Protocols Dry Lab Protocol
– Image Acquisition Protocol
– Feature Extraction Protocol
Wet Lab Protocols – Hybridization Protocols
– Labeling Protocols
Batch Upload
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New Experiment – Step 7 Hybridizations continued…
– Common Hybridization Information
Array Design– Created in the Array
Design Tab• NCICB_Mus
musculus_1.1_19K Manufacture
– Who makes the hybridization
• Not Utilized at this time Number of Hybridizations
– How many hybridizations are you going to add to your experiment
Hybridization Protocol– Wet Lab Protocol created
in the Protocol Tab Select Next
ExperimentNew Experiment
Step 7 – Hybridizations continued…
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ExperimentNew Experiment
Step 7 – Hybridizations continued…
New Experiment – Step 7 Hybridizations continued…
– Verify the information on the Hybridization is correct
NOTE: This information comes from the completion of the Array Design as well as the Protocol (Hybridization Protocol = Wet Lab Protocol)
– If the Array Design Information has not been completed return to the Array Design tab to complete the information.
– If the Wet Lab/Hybridization Protocol has not been completed return to the Protocol Tab to complete the information
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ExperimentNew Experiment
Step 7 – Hybridizations continued…
New Experiment – Step 7 Hybridizations continued…
– Performer The person who
created the hybridization
– Jamie Keller– Activity Date
Date the Experiment is being submitted/added
– 10/18/2004 Select Next
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New Experiment – Step 7 Hybridizations continued…
– Identifying Image Acquisition Protocol
This is the Wet Lab Protocol created in the Protocol Tab
If the Image Acquisition Protocol/Wet Lab Protocol is missing return to the Protocol Tab to create it
Select Next
ExperimentNew Experiment
Step 7 – Hybridizations continued…
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New Experiment – Step 7 Hybridizations continued…
– Verify the information on the Protocol is correct
NOTE: This information comes from the completion of the Image Acquisition/ Wet Lab Protocol
– Lab Performer The person who created the
hybridization– Jamie Keller
– Activity Date Date in which the
Experiment is being submitted/added
– 10/18/2004
Select Next
ExperimentNew Experiment
Step 7 – Hybridizations continued…
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ExperimentNew Experiment
Step 7 – Hybridizations continued…
New Experiment – Step 7 Hybridizations continued…
– Identifying Feature Extraction Protocol
This is the Dry Lab Protocol created in the Protocol Tab
If the Feature Extraction Protocol/Dry Lab Protocol is missing return to the Protocol Tab to create it
Select Next
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New Experiment – Step 7 Hybridizations continued…
– Verify the information on the Protocol is correct
NOTE: This information comes from the completion of the Feature Extraction/ Dry Lab Protocol
– Lab Performer The person who created
the hybridization– Jamie Keller
– Activity Date Date in which the
experiment is being submitted/added
– 10/18/2004 Select Next
ExperimentNew Experiment
Step 7 – Hybridizations continued…
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ExperimentNew Experiment
Step 7 – Hybridizations continued…
New Experiment – Step 7 Hybridizations continued…
– Identifying Additional Hybridization Information
Associate files, documents, etc. with the Hybridization
Select Next to create New Experiment
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ExperimentNew Experiment
Step 7 – Hybridizations continued…
New Experiment – Step 7 Hybridizations continued…
– Verify the Experiment is being processed
This may take a few minutes
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ExperimentNew Experiment
Step 7 – Hybridizations continued…
New Experiment – Step 7 Hybridizations continued…
– Continue The Experiment has
now been added/submitted to caArray!!!
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ExperimentNew Experiment
Step 8 – MAGE ML Download
New Experiment – Step 8 MAGE ML Download
– MAGE ML Download Once the Experiment has
been added to caArray a MAGE ML file can be generated
– NOTE: This is a Snap shot in time, if modifications or changes are made to the experiment the MAGE ML must be generated again to capture the updates