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docs/01-intro.md

@@ -13,7 +13,7 @@ Check out the video below. It provides a summary of the introduction to this cou
 
 First, we will discuss the motivations behind the new data management and sharing policy. This policy is applicable for (most) grant proposals submitted to the NIH as of January 25, 2023.
 
-<img src="resources/images/01-intro_files/figure-html//1luFoDzF6aDJEebbL6iWoJ_s8s9nQnaWLL5jghbmWdak_g16b04bd80e5_1_103.png" title="We are on the first step of the pathway- understanding the motivations of the policy." alt="We are on the first step of the pathway- understanding the motivations of the policy." width="80%" style="display: block; margin: auto;" />
+<img src="resources/images/01-intro_files/figure-html//1luFoDzF6aDJEebbL6iWoJ_s8s9nQnaWLL5jghbmWdak_g16b04bd80e5_1_103.png" alt="We are on the first step of the pathway- understanding the motivations of the policy." width="80%" style="display: block; margin: auto;" />
 
 Why is the NIH doing this? There are several reasons why sharing data can be beneficial to the scientific community.
 
@@ -26,7 +26,7 @@ Why is the NIH doing this? There are several reasons why sharing data can be ben
 - **Collaboration opportunities** - Available data can inspire other researchers to explore new directions or extend upon previous work. These researchers might reach out to collaborate.
 - **Data citations** - Due to the importance of data generation and sharing to the NIH, data will now be seen as research product that demonstrates a contribution to the scientific community.
 
-<img src="resources/images/01-intro_files/figure-html//1luFoDzF6aDJEebbL6iWoJ_s8s9nQnaWLL5jghbmWdak_g29f8bf18fa1_80_0.png" title="Scientist examines the result of a plate assay, which is a test that allows scientists to count how many flu virus particles (virions) are in a mixture" alt="Scientist examines the result of a plate assay, which is a test that allows scientists to count how many flu virus particles (virions) are in a mixture" width="80%" style="display: block; margin: auto;" />
+<img src="resources/images/01-intro_files/figure-html//1luFoDzF6aDJEebbL6iWoJ_s8s9nQnaWLL5jghbmWdak_g29f8bf18fa1_80_0.png" alt="Scientist examines the result of a plate assay, which is a test that allows scientists to count how many flu virus particles (virions) are in a mixture" width="80%" style="display: block; margin: auto;" />
 
 ## Key terms 
 
@@ -72,7 +72,7 @@ Check out the video below. It provides a summary of the personal considerations
 
 > You can refer to the [NIH overview](https://sharing.nih.gov/data-management-and-sharing-policy/about-data-management-and-sharing-policy/research-covered-under-the-data-management-sharing-policy#after){target="_blank"} of which research will be covered by this new policy.  
 
-<img src="resources/images/01-intro_files/figure-html//1luFoDzF6aDJEebbL6iWoJ_s8s9nQnaWLL5jghbmWdak_g16b04bd80e5_4_12.png" title="We are on the second step of the pathway - personal considerations of the policy." alt="We are on the second step of the pathway - personal considerations of the policy." width="80%" style="display: block; margin: auto;" />
+<img src="resources/images/01-intro_files/figure-html//1luFoDzF6aDJEebbL6iWoJ_s8s9nQnaWLL5jghbmWdak_g16b04bd80e5_4_12.png" alt="We are on the second step of the pathway - personal considerations of the policy." width="80%" style="display: block; margin: auto;" />
 
 The major requirement of the policy is that all grant proposals (submitted after January 25th, 2023) for mechanisms that require compliance, **must include a plan** for how they will manage and share their data. 
 
@@ -119,11 +119,11 @@ You can look up your NIH Activity Code [here](https://sharing.nih.gov/node/112){
 
 For example, I am interested in applying to a **R03** award.
 
-<img src="resources/images/01-intro_files/figure-html//1luFoDzF6aDJEebbL6iWoJ_s8s9nQnaWLL5jghbmWdak_g1740f401082_0_56.png" title="I can find the R03 activity code in the request for applications." alt="I can find the R03 activity code in the request for applications." width="100%" style="display: block; margin: auto;" />
+<img src="resources/images/01-intro_files/figure-html//1luFoDzF6aDJEebbL6iWoJ_s8s9nQnaWLL5jghbmWdak_g1740f401082_0_56.png" alt="I can find the R03 activity code in the request for applications." width="100%" style="display: block; margin: auto;" />
 
 According to the table, a **DMS Plan is required** for this particular award.
 
-<img src="resources/images/01-intro_files/figure-html//1luFoDzF6aDJEebbL6iWoJ_s8s9nQnaWLL5jghbmWdak_g1740f401082_0_64.png" title="I can determine if a DMS plan is required using the table here: https://sharing.nih.gov/sites/default/files/List-of-Activity-Codes-Applicable-to-DMS-Policy.pdf" alt="I can determine if a DMS plan is required using the table here: https://sharing.nih.gov/sites/default/files/List-of-Activity-Codes-Applicable-to-DMS-Policy.pdf" width="100%" style="display: block; margin: auto;" />
+<img src="resources/images/01-intro_files/figure-html//1luFoDzF6aDJEebbL6iWoJ_s8s9nQnaWLL5jghbmWdak_g1740f401082_0_64.png" alt="I can determine if a DMS plan is required using the table here: https://sharing.nih.gov/sites/default/files/List-of-Activity-Codes-Applicable-to-DMS-Policy.pdf" width="100%" style="display: block; margin: auto;" />
 
 ### Data-generating Research {#scientific-data}
 
@@ -133,7 +133,7 @@ Does my research generate scientific data?
 
 The NIH Data Management and Sharing (DMS) Policy applies to **all NIH-supported research generating scientific data**. But what is "scientific data"?
 
-<img src="resources/images/01-intro_files/figure-html//1luFoDzF6aDJEebbL6iWoJ_s8s9nQnaWLL5jghbmWdak_g1740f401082_0_0.png" title="Scientific data should be shared under the new DMS policy, but there are many scientific products that are not considered scientific data." alt="Scientific data should be shared under the new DMS policy, but there are many scientific products that are not considered scientific data." width="70%" style="display: block; margin: auto;" />
+<img src="resources/images/01-intro_files/figure-html//1luFoDzF6aDJEebbL6iWoJ_s8s9nQnaWLL5jghbmWdak_g1740f401082_0_0.png" alt="Scientific data should be shared under the new DMS policy, but there are many scientific products that are not considered scientific data." width="70%" style="display: block; margin: auto;" />
 
 #### Scientific data
 
@@ -214,7 +214,7 @@ Is it possible to not share data?
 
 There are legitimate reasons you might not share your data. Data might not be shareable due to ethical, legal, or technical concerns. **You will still need to submit a DMS Plan even if you plan to withhold data sharing**. You must explain your reasoning in your DMS Plan.
 
-<img src="resources/images/01-intro_files/figure-html//1luFoDzF6aDJEebbL6iWoJ_s8s9nQnaWLL5jghbmWdak_g1740f401082_0_36.png" title="Researchers with scientific data must justify why they will not share data with an appropriate exception." alt="Researchers with scientific data must justify why they will not share data with an appropriate exception." width="70%" style="display: block; margin: auto;" />
+<img src="resources/images/01-intro_files/figure-html//1luFoDzF6aDJEebbL6iWoJ_s8s9nQnaWLL5jghbmWdak_g1740f401082_0_36.png" alt="Researchers with scientific data must justify why they will not share data with an appropriate exception." width="70%" style="display: block; margin: auto;" />
 
 Justifiable ethical, legal, and technical factors for limiting sharing of data include: 
 

docs/02-data_management_plan.md

@@ -28,7 +28,7 @@ We will cover specific requirements for each of these sections later. However, b
 
 To enable a more productive research experience and to ease your future compliance with any data sharing requirements, active data management during the research process can be very helpful.  
 
-<img src="resources/images/02-data_management_plan_files/figure-html//1luFoDzF6aDJEebbL6iWoJ_s8s9nQnaWLL5jghbmWdak_g16b04bd80e5_4_37.png" title="We are on the third step of the pathway - Data Storage Options." alt="We are on the third step of the pathway - Data Storage Options." width="80%" style="display: block; margin: auto;" />
+<img src="resources/images/02-data_management_plan_files/figure-html//1luFoDzF6aDJEebbL6iWoJ_s8s9nQnaWLL5jghbmWdak_g16b04bd80e5_4_37.png" alt="We are on the third step of the pathway - Data Storage Options." width="80%" style="display: block; margin: auto;" />
 
 ## Data Storage Concerns
 
@@ -50,7 +50,7 @@ Your data storage needs will depend greatly on the type of data you will be work
 | Clinical trials | 2-25 MB |
 
 
-<img src="resources/images/02-data_management_plan_files/figure-html//1luFoDzF6aDJEebbL6iWoJ_s8s9nQnaWLL5jghbmWdak_g18159f1730a_67_0.png" title="A cell phone with 64GB of storage can fit 1 WGS file, 2 RNA-seq files, 25 imaging files, and thousands of flow cytometry, clinical trial, microscopy, and proteomics files." alt="A cell phone with 64GB of storage can fit 1 WGS file, 2 RNA-seq files, 25 imaging files, and thousands of flow cytometry, clinical trial, microscopy, and proteomics files." width="80%" style="display: block; margin: auto;" />
+<img src="resources/images/02-data_management_plan_files/figure-html//1luFoDzF6aDJEebbL6iWoJ_s8s9nQnaWLL5jghbmWdak_g18159f1730a_67_0.png" alt="A cell phone with 64GB of storage can fit 1 WGS file, 2 RNA-seq files, 25 imaging files, and thousands of flow cytometry, clinical trial, microscopy, and proteomics files." width="80%" style="display: block; margin: auto;" />
 
 As you can see some of these data types require large data files. These files may quickly add up to require more storage or computing capacity than your laptop (which typically have 250 GB-1 TB of storage)! If you want to learn more about data file sizes check out the [data file size details section](https://hutchdatascience.org/NIH_Data_Sharing/data-file-size-details.html) of the appendix and this class on [Computing for Cancer Informatics](https://jhudatascience.org/Computing_for_Cancer_Informatics/index.html) from the [Informatics Technology for Cancer Research (ITCR)](https://itcr.cancer.gov/) [Training Network (ITN)](https://www.itcrtraining.org/) for options on how to manage large data files.
 
@@ -65,7 +65,7 @@ Some programs or Funding Opportunity Announcements (FOA) will specify where the
 
 Other programs or FOAs will not specify where the data should be shared, however the NIH provides an [interactive table of NIH-supported data repositories](https://sharing.nih.gov/data-management-and-sharing-policy/sharing-scientific-data/repositories-for-sharing-scientific-data) to help you identify repositories that might be appropriate for your data. 
 
-<img src="resources/images/02-data_management_plan_files/figure-html//1luFoDzF6aDJEebbL6iWoJ_s8s9nQnaWLL5jghbmWdak_g18159f1730a_67_39.png" title="The interactive table provided by NIH can help you find an appropriate repository." alt="The interactive table provided by NIH can help you find an appropriate repository." width="80%" style="display: block; margin: auto;" />
+<img src="resources/images/02-data_management_plan_files/figure-html//1luFoDzF6aDJEebbL6iWoJ_s8s9nQnaWLL5jghbmWdak_g18159f1730a_67_39.png" alt="The interactive table provided by NIH can help you find an appropriate repository." width="80%" style="display: block; margin: auto;" />
 
 If you don't find a repository there, additional repositories can also be found at the following links:
 
@@ -151,7 +151,7 @@ What if I can't find an appropriate repository?
 
 Note that the NIH encourages that an existing data sharing repository be used whenever one is available instead of one of these options.
 
-<img src="resources/images/02-data_management_plan_files/figure-html//1luFoDzF6aDJEebbL6iWoJ_s8s9nQnaWLL5jghbmWdak_g18159f1730a_44_28.png" title="NIH prefers you to use the explicitly mentioned repository, followed by a known, FAIR repository, followed by a public generalist repository for data storage." alt="NIH prefers you to use the explicitly mentioned repository, followed by a known, FAIR repository, followed by a public generalist repository for data storage." width="80%" style="display: block; margin: auto;" />
+<img src="resources/images/02-data_management_plan_files/figure-html//1luFoDzF6aDJEebbL6iWoJ_s8s9nQnaWLL5jghbmWdak_g18159f1730a_44_28.png" alt="NIH prefers you to use the explicitly mentioned repository, followed by a known, FAIR repository, followed by a public generalist repository for data storage." width="80%" style="display: block; margin: auto;" />
 
 ## Summary
 

docs/03-budgeting.md

@@ -5,11 +5,11 @@
 In this section we will describe what you need to think about in terms of how to budget for the management and sharing of your data, as well as what money you can request to help you carry out your DMS plans.
 
 
-<img src="resources/images/03-budgeting_files/figure-html//1luFoDzF6aDJEebbL6iWoJ_s8s9nQnaWLL5jghbmWdak_g16b04bd80e5_4_62.png" title="We are on the fourth step of the pathway - Budgeting." alt="We are on the fourth step of the pathway - Budgeting." width="80%" style="display: block; margin: auto;" />
+<img src="resources/images/03-budgeting_files/figure-html//1luFoDzF6aDJEebbL6iWoJ_s8s9nQnaWLL5jghbmWdak_g16b04bd80e5_4_62.png" alt="We are on the fourth step of the pathway - Budgeting." width="80%" style="display: block; margin: auto;" />
 
 > You can refer to the [NIH overview about budgeting for this policy](https://sharing.nih.gov/data-management-and-sharing-policy/planning-and-budgeting-DMS/budgeting-for-data-management-sharing#after){target="_blank"} of which research will be covered by this new policy.  
 
-<img src="resources/images/03-budgeting_files/figure-html//1luFoDzF6aDJEebbL6iWoJ_s8s9nQnaWLL5jghbmWdak_g178800e11b1_15_16.png" title="Costs associated with FAIR principles are generally allowed, while infrastructure and data gathering costs are not." alt="Costs associated with FAIR principles are generally allowed, while infrastructure and data gathering costs are not." width="80%" style="display: block; margin: auto;" />
+<img src="resources/images/03-budgeting_files/figure-html//1luFoDzF6aDJEebbL6iWoJ_s8s9nQnaWLL5jghbmWdak_g178800e11b1_15_16.png" alt="Costs associated with FAIR principles are generally allowed, while infrastructure and data gathering costs are not." width="80%" style="display: block; margin: auto;" />
 
 ## Allowable Costs
 

docs/04-writing_a_DMS_plan.md

@@ -5,7 +5,7 @@
 
 In this section we will guide you through the requirements for the various sections of the DMS plan.
 
-<img src="resources/images/04-writing_a_DMS_plan_files/figure-html//1luFoDzF6aDJEebbL6iWoJ_s8s9nQnaWLL5jghbmWdak_g16b04bd80e5_4_88.png" title="We are on the fifth step of the pathway- Creating a DMS plan." alt="We are on the fifth step of the pathway- Creating a DMS plan." width="80%" />
+<img src="resources/images/04-writing_a_DMS_plan_files/figure-html//1luFoDzF6aDJEebbL6iWoJ_s8s9nQnaWLL5jghbmWdak_g16b04bd80e5_4_88.png" alt="We are on the fifth step of the pathway- Creating a DMS plan." width="80%" />
 
 <div class = "notice"> 
 
@@ -27,7 +27,7 @@ The Fred Hutch Data Science Lab has created and online app where you can create
 
 https://dmshelper.fredhutch.org/
 
-<img src="resources/images/04-writing_a_DMS_plan_files/figure-html//1luFoDzF6aDJEebbL6iWoJ_s8s9nQnaWLL5jghbmWdak_g21c2a6e60cf_39_0.png" title="Preview of the DMS Helper App." alt="Preview of the DMS Helper App." width="100%" style="display: block; margin: auto;" />
+<img src="resources/images/04-writing_a_DMS_plan_files/figure-html//1luFoDzF6aDJEebbL6iWoJ_s8s9nQnaWLL5jghbmWdak_g21c2a6e60cf_39_0.png" alt="Preview of the DMS Helper App." width="100%" style="display: block; margin: auto;" />
 
 <div class = "notice"> 
 
@@ -62,7 +62,7 @@ You are encouraged to talk to the appropriate Program Officer for your respectiv
 
 - _Keep in mind that your DMS plan will **not** be reviewed by reviewers, only the budget sections in regard to this will be seen by them. Instead the Program Officer will review your DMS plan to determine if it is reasonable and appropriate or if you need to make changes._
 
-<img src="resources/images/04-writing_a_DMS_plan_files/figure-html//1luFoDzF6aDJEebbL6iWoJ_s8s9nQnaWLL5jghbmWdak_g18159f1730a_67_87.png" title="When writing the plan, ensure it is less than 2 pages long, contains no confidential information, and has been planned out carefully, contacting the program officer if necessary." alt="When writing the plan, ensure it is less than 2 pages long, contains no confidential information, and has been planned out carefully, contacting the program officer if necessary." width="80%" style="display: block; margin: auto;" />
+<img src="resources/images/04-writing_a_DMS_plan_files/figure-html//1luFoDzF6aDJEebbL6iWoJ_s8s9nQnaWLL5jghbmWdak_g18159f1730a_67_87.png" alt="When writing the plan, ensure it is less than 2 pages long, contains no confidential information, and has been planned out carefully, contacting the program officer if necessary." width="80%" style="display: block; margin: auto;" />
 
 ##  Data Type
 

docs/05-submission.md

@@ -9,7 +9,7 @@
 
 In this section we will outline how you can submit your DMS plan: 
 
-<img src="resources/images/05-submission_files/figure-html//1luFoDzF6aDJEebbL6iWoJ_s8s9nQnaWLL5jghbmWdak_g16b04bd80e5_4_113.png" title="We are on the sixth step of our pathway - Submission" alt="We are on the sixth step of our pathway - Submission" width="80%" />
+<img src="resources/images/05-submission_files/figure-html//1luFoDzF6aDJEebbL6iWoJ_s8s9nQnaWLL5jghbmWdak_g16b04bd80e5_4_113.png" alt="We are on the sixth step of our pathway - Submission" width="80%" />
 
 ## Submission by Funding Type
 
@@ -37,7 +37,7 @@ It is important to note that the submission process may be different depending o
 
 In this section we will discuss tips about what might be needed after you submit your DMS plan: 
 
-<img src="resources/images/05-submission_files/figure-html//1luFoDzF6aDJEebbL6iWoJ_s8s9nQnaWLL5jghbmWdak_g16b04bd80e5_4_138.png" title="We are on the final step of our pathway - Post Submission" alt="We are on the final step of our pathway - Post Submission" width="100%" />
+<img src="resources/images/05-submission_files/figure-html//1luFoDzF6aDJEebbL6iWoJ_s8s9nQnaWLL5jghbmWdak_g16b04bd80e5_4_138.png" alt="We are on the final step of our pathway - Post Submission" width="100%" />
 
 - You can update your DMS plan if is not accepted during the [Just-in-Time](https://grants.nih.gov/grants/policy/nihgps/HTML5/section_2/2.5.1_just-in-time_procedures.htm) process.
 - You can also update your DMS plan during regular reporting intervals, but these changes will need to be approved by program staff. Researchers are encouraged to discuss such changes in advance.
@@ -48,7 +48,7 @@ In this section we will discuss tips about what might be needed after you submit
 - Investigators are expected to report progress made on data sharing in their annual Research Progress Performance Report (RPPR).
    - NIH staff will monitor compliance with the DMS plan during this process.
 
-<img src="resources/images/05-submission_files/figure-html//1luFoDzF6aDJEebbL6iWoJ_s8s9nQnaWLL5jghbmWdak_g18159f1730a_67_115.png" title="DMS plans can be edited during the Just In Time process or during regular reporting intervals, so it is okay if you need to make changes when you learn of better alternatives." alt="DMS plans can be edited during the Just In Time process or during regular reporting intervals, so it is okay if you need to make changes when you learn of better alternatives." width="100%" />
+<img src="resources/images/05-submission_files/figure-html//1luFoDzF6aDJEebbL6iWoJ_s8s9nQnaWLL5jghbmWdak_g18159f1730a_67_115.png" alt="DMS plans can be edited during the Just In Time process or during regular reporting intervals, so it is okay if you need to make changes when you learn of better alternatives." width="100%" />
 
 # Video Creating Your Plan Wrap Up