Merge pull request #76 from fhdsl/updates

adding some more images

03-Data_Security.Rmd

@@ -248,9 +248,7 @@ Data is masked and kept secure by different protocols. Two that are quite common
 
 Where SSL is for moving data from a website to a server, SSH is for making connections to execute commands on remote computers.
 
-```{r, fig.align='center', echo = FALSE, fig.alt= "SSL vs SSH SSL has cryptographic tunneling protocol and has a username/password authentication system. SSL does not have a username/password authentication system like SSH. SSH completely depends on the network tunneling. SSL is asynchronous as it depends on the certificates. SSH is appropriate and effective for securely executing commands across the internet.", out.width="100%"}
-ottrpal::include_slide("https://docs.google.com/presentation/d/1SRokLaGAc2hiwJSN26FHE0ZEEhPr3KQdyMICic8kAcs/edit#slide=id.g2134f5bcd65_0_0")
-```
+
 
 #### SSL Socket Layer
 
@@ -266,9 +264,11 @@ According to @digicert this involves the following steps:
 
 Note that newer versions of this process are called Transport Layer Security (TLS).
 
+
+
 #### SSH Secure Shell
 
-SSH (secure shell) is also a process for securely transmitting files from one computer to another using encryption. However, in this case it can be done using a command line interface instead of a browser. SSH also does not involve certificates.
+SSH (secure shell) is also a process for securely transmitting files from one computer to another using encryption. However, in this case it can be done using a command line interface instead of a browser. SSH does not involve certificates.
 
 SSH is used for communicating to remote computers which is why it is commonly used at institutions to get access to high powered computing clusters.
 
@@ -283,6 +283,10 @@ SSH works like this[@sshprotocol]:
 ottrpal::include_slide("https://docs.google.com/presentation/d/1SRokLaGAc2hiwJSN26FHE0ZEEhPr3KQdyMICic8kAcs/edit#slide=id.g2134f5bcd65_0_14")
 ```
 
+```{r, fig.align='center', echo = FALSE, fig.alt= "SSL vs SSH SSL has cryptographic tunneling protocol and has a username/password authentication system. SSL does not have a username/password authentication system like SSH. SSH completely depends on the network tunneling. SSL is asynchronous as it depends on the certificates. SSH is appropriate and effective for securely executing commands across the internet.", out.width="100%"}
+ottrpal::include_slide("https://docs.google.com/presentation/d/1SRokLaGAc2hiwJSN26FHE0ZEEhPr3KQdyMICic8kAcs/edit#slide=id.g2134f5bcd65_0_0")
+```
+
 For more about SSH and SSL:
 
 - [SSH and SSL exploring the similarities and differences](https://sectigostore.com/blog/ssh-vs-ssl-exploring-the-similarities-and-differences/)

05-Data_Ethics.Rmd

@@ -58,6 +58,12 @@ While data sharing can result in wonderful opportunities for secondary analysis,
 Overall there is a continuum of risk across the various types of data that we as researchers collect. Wile some forms of data, such as that derived from model organisms pose essentially no risk, intermediate forms of data such as summarized counts across a set of human samples pose more risk, while raw data and in particular data from individuals such as whole genome sequencing data, pose great risk for identification [@byrd_responsible_2020].
 
 
+```{r, fig.align='center', echo = FALSE, fig.alt= "re-identification risk is on a continuum. The image shows a double sided arrow that goes from green to red with the green side showing model organism data and the red side showing whole genome sequencing. It offers suggestsions for sharing different types of data, with public access to anyone for model organism data and images of internal tissues, public sharing of processed data for whole genome somatic varaints and RNA-Seq (expression estimates), Aggregate group sharing of data from exome-seq and DNA methylation data  and controlled access (only for certain people) for whole genome germline data", out.width="100%"}
+ottrpal::include_slide("https://docs.google.com/presentation/d/1SRokLaGAc2hiwJSN26FHE0ZEEhPr3KQdyMICic8kAcs/edit#slide=id.g302b08a6790_0_0")
+```
+
+
+
 ### Why does it mater that research subjects might be identifiable to others?
 
 In some cases open awareness about patients with certain types of cancers or diseases can be useful to allow other researchers and patients to find these individuals to encourage additional research and patient support group participation (especially for rare diseases or conditions).
@@ -202,10 +208,11 @@ We have already talked about the concept of informed consent. Obtaining consent
   - Individuals should be made aware of the uncertainty associated with risks and benefits
   - Individuals should have the capacity to understand the risks and benefits (this involves consideration for language barriers, intellectual capacity, emotional capacity, stress, sleep loss and other forms of physical strain)
   - Individuals should be able to withdraw consent at anytime
-  - Individuals should be respected through-out the process including consideration for the cultural values of the recruited populations
+  - Individuals should be respected throughout the process including consideration for the cultural values of the recruited populations
   - Consent forms and processes should be reviewed by people with diverse expertise, such as understanding of ethics, equity, and patients and community experience
 
 
+
 ## Medical Ethics Timeline
 
 It is helpful to get a sense of the timing when society established ethical medical standards and laws. Here we will point out important events in the timeline of medical ethics, with an emphasis on the United States.