IMDS Tutorial

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IMDS Tutorial

• Integrated Microarray Database System

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IMDS User Interface Functions

1. Logging in to the database.
2. Entering a new experiment.
3. Searching for experiments.
4. Updating an experiment.
5. Entering new sources.
6. Entering new treatment categories.
7. Reviewing the file access log.

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I. Logging in to the database

• Enter username and password and click on the
  Submit button.
• An introductory page will appear, with Welcome
  your name at the top.

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I. Logon Screen
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I. Introductory Page
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II. Entering a New Experiment

• Click on the experiment list link on the sidebar
  menu. You will be taken to the experiment list
  page.
• Click on Create a New Experiment . You will be
  taken to the experiment creation page.

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II. Experiment List Link
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II. Create a New Experiment
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II. Experiment Creation Page
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II. Entering a New Experiment

• Enter the information describing the experiment
  section 1.
• Enter the information about the treatments used
  in the experiment section 2.
• Enter the information about the samples used in
  the experiment section 3.
• Enter the information about the arrays used in
  the experiment section 4.
• Upload the files (raw data) for the experiment
  section 5.
• Upload the files (analyzed data and general
  information) for the experiment section 6.

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II. Entering a New Experiment Section 1
(Description)

• Enter the experiment name and a short abstract in
  the fields marked name and description.
• Enter the starting date for the experiment. For
  example, 03/31/03 or 03/31/2003.
• Select your research site and PI from the pull
  down menus.
• Select the type of experiment from the pull down
  menus. Select other if your experiment type is
  not listed.
• Click on the Submit button when you are
  finished. You will be taken back to the
  experiment list page.

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II. Entering a New Experiment Section 1
(Description)
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II. Entering a New Treatment Section 2
(Treatment List)

• From the experiment list page, click on the name
  of the experiment for which you want to enter a
  new treatment.
• From the description page for that experiment,
  click on the Treatment List link in the footer.
  You will be taken to the treatment creation
  page.

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II. Entering a New Treatment Section 2
(Treatment List)
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II. Entering a New Treatment Section 2
(Treatment List)
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II. Entering a New Treatment Section 2
(Treatment Creation Page)
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II. Entering a New Treatment Section 2
(Treatment Creation Page)

• Enter the treatment name and a short treatment
  description or treatment protocol in the fields
  marked Treatment Name and Treatment Description.
• Select your treatment category from the pull down
  menu.
• Click on the Submit button when you are
  finished. You will be taken back to the
  treatment list page.

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II. Entering a New Treatment Section 2
(Treatment Creation Page)
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II. Entering a New Treatment Section 2
(Treatment Creation Page)
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II. Entering a New Treatment Section 2
(Treatment List Page)
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II. Entering a New Sample Section 3 (Sample
List)

• From the treatment list page (or from the
  description page for your experiment), click on
  the Sample List link in the footer. You will
  be taken to the sample list page.
• Click on Create a New Sample . You will be
  taken to the sample creation page.

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II. Entering a New Sample Section 3 (Sample
List)
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II. Entering a New Sample Section 3 (Sample
List)
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II. Entering a New Sample Section 3 (Sample
Creation Page)
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II. Entering a New Sample Section 3 (Sample
Creation Page)

• Enter the sample name and a short description in
  the fields marked Sample Name and Sample
  Description.
• Select the source for the sample from the pull
  down menu.
• Click on the Submit button when you are
  finished. You will be taken back to the sample
  list page.

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II. Entering a New Array Section 4 (Array List)

• From the sample list page (or from the
  description page for your experiment, or the
  treatment list page), click on the Array List
  link in the footer. You will be taken to the
  array list page.
• Click on Create a New Array . You will be
  taken to the array creation page.

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II. Entering a New Array Section 4 (Array List)
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II. Entering a New Array Section 4 (Array List)
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II. Entering a New Array Section 4 (Array
Creation Page)
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II. Entering a New Array Section 4 (Array
Creation Page)

• Enter the array name and a short description in
  the fields marked Array Name and Array
  Description.
• Select the array type for the array from the pull
  down menu (Affymetrix, spotted array-cDNA,
  spotted array-oligo, other).
• Select the genus species and genotype used to
  make the array (the probe) from the pull down
  menus. This is the genus species spotted on the
  array itself, not the sample (source) hybridized
  to the array (target). Type in the strain used
  to make the array (if applicable). Again, this
  entry refers to the spots on the array and not
  the sample hybridized to the array.

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II. Entering a New Array Section 4 (Array
Creation Page)

• Select the sample used to make the array from the
  pull down menu. This entry refers to the target
  hybridized to the array.
• Similarly, select the treatment used to make the
  array from the pull down menu. Enter the
  treatment time as text below.
• Enter a comment (excellent, good, slightly
  degraded, etc.) about the quality of the RNA
  extracted from the sample.
• Click on the Submit button when you are
  finished. You will be taken back to the array
  list page.

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II. Entering a New Array Section 4 (Array
Creation Page)
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II. Entering a New Array Section 4 (Array
Creation Page)
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II. Entering a New Array Section 4 (Array List
Page)
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II. Uploading Array Files (raw data) Section 5
(Array List)

• From the array list page, click on the name of
  the array for which you wish to upload raw data
  files. You will be taken to the array display
  page.
• Click on Add New File To Array Array Name.
  You will be taken to the array file creation
  page.
• Click on the Browse button to locate the file on
  your hard disk or CD.
• Click on the Upload button to upload your file to
  the IMDS database.

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II. Uploading Array Files (raw data) Section 5
(Array Display)
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II. Uploading Array Files (raw data) Section 5
(Array File Creation)
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II. Uploading Array Files (raw data) Section 5
(Array File Creation)
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II. Uploading Array Files (raw data) Section 5
(Array Upload)
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II. Uploading Analyzed Data Files Section 6
(File List)

• From the description page for your experiment (or
  from the treatment list page, sample list page or
  array list page), click on the file list link on
  the footer. You will be taken to the experiment
  file list page.
• Click on Add New File To Experiment Experiment
  Name. You will be taken to the experiment file
  creation page.

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II. Uploading Analyzed Data Files Section 6
(File List)
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II. Uploading Analyzed Data Files Section 6
(Experiment File Creation)
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II. Uploading Analyzed Data Files Section 6
(Experiment File Creation)
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II. Uploading Analyzed Data Files Section 6
(Experiment Upload)
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II. Uploading Other Experimental Files Section
6 (File List)

• From the description page for your experiment (or
  from the treatment list page, sample list page or
  array list page), click on the file list link on
  the footer. You will be taken to the experiment
  file list page.
• Click on Add New File To Experiment Experiment
  Name. You will be taken to the experiment file
  creation page.

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II. Uploading Other Experimental Files Section
6 (File List)
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II. Uploading Other Experimental Files Section
6 (Experiment File Creation)
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II. Uploading Other Experimental Files Section
6 (Experiment File Creation)
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II. Uploading Other Experimental Files Section
6 (Experiment upload)
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III. Searching for experiments

• Click on the Search Experiments link on the
  sidebar menu. You will be taken to the main
  search page.
• Click on the search criteria that you want to
  use. For this example, let us suppose that you
  would like to retrieve experiments that use a
  certain source. You would click on Source
  (Target). You would then be taken to the single
  search page, where you would chose from the
  sources in a drop down menu that represent the
  sources listed in the database. You would then
  click search to retrieve the results.

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III. Searching for experiments
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III. Searching for experiments
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III. Searching for experiments
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III. Searching for experiments
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III. Searching for experiments
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III. Searching for experiments

• The results page returns the following
  information about an experiment experiment
  name, investigator, genomics site, starting date,
  experiment type, source (target), mutant name
  (target), strain (target), source /catalog number
  (target), genus species (target), genotype
  (target), ecotype (target), organ (target),
  tissue (target), treatment category, array type,
  genus species used to make array (probe),
  genotype used to make array (probe), strain used
  to make array (probe).
• Clicking on the experiment name takes you to the
  description page for that experiment. From this
  page, all information for the experiment can be
  accessed, including the download of raw array
  data and analyzed experimental data.

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III. Searching for experiments
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IV. Updating an experiment

• From either the experiment list page (accessed by
  clicking on the experiment list link in the
  sidebar menu) or through the search experiments
  function, you can locate a specific experiment to
  update.
• The description, treatment list, sample list,
  array list or file list can be updated for a
  given experiment by simply clicking on the
  parameter that you wish to update. You will be
  taken to a page that will display the current
  parameters and allow you to edit them. Finish by
  clicking on the update button.

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V. Entering new sources

• Click on the source list link on the sidebar
  menu. You will be taken to the experiment list
  page.
• Click on Create a New Source. You will be
  taken to the source creation page.

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V. Entering new sources
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V. Entering new sources
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V. Entering new sources
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V. Entering new sources

• Enter the source name and a short description in
  the fields marked name and description.
• If applicable, enter mutant type, mutant name,
  strain and source/catalog number in the
  respective fields. If not applicable, enter N/A.
• Select the genus species, genotype, ecotype,
  organ and tissue from the pull down menus.
• Click on the Submit button when you are
  finished. You will be taken back to the source
  list page.

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VI. Entering new treatment categories

• Click on the treatment categories link on the
  sidebar menu. You will be taken to the treatment
  list page.
• Click on Create a New Treatment Category. You
  will be taken to the treatment creation page.

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VI. Entering new treatment categories
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VI. Entering new treatment categories
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VI. Entering new treatment categories
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VI. Entering new treatment categories

• Enter the treatment category name and a short
  description in the fields marked name and
  description.
• Click on the Submit button when you are
  finished. You will be taken back to the
  treatment category list page.

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VII. Reviewing the file access log.

• Click on the file access log link on the sidebar
  menu. You will be taken to the file access list
  page.
• The file access list page shows which user
  accessed the database (user name), whether the
  user wrote to or read from the database (access
  type), the date and time of access, and the
  accessed file name.

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VII. Reviewing the file access log.
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VII. Reviewing the file access log.