Last updated: 2020-06-08
Checks: 7 0
Knit directory: bioinformatics_tips/
This reproducible R Markdown analysis was created with workflowr (version 1.6.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.
Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.
Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.
The command set.seed(20200503) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.
Great job! Recording the operating system, R version, and package versions is critical for reproducibility.
Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.
Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.
Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.
The results in this page were generated with repository version 9019e42. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.
Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:
Ignored files:
Ignored: .DS_Store
Ignored: .Rhistory
Ignored: .Rproj.user/
Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.
These are the previous versions of the repository in which changes were made to the R Markdown (analysis/security.Rmd) and HTML (docs/security.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.
| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 9019e42 | davetang | 2020-06-08 | Shared-key cryptosystem |
| html | f851e18 | davetang | 2020-06-07 | Build site. |
| Rmd | a36c1e8 | davetang | 2020-06-07 | Security basics |
The Internet has become an integral part of our lives. When exchanging data over the internet, the data passes through various networks and devices. There are four problems that can occur when data is transferred from one party to another:
These four problems are countered by:
Encryption means performing an operation on data such that a computer cannot decipher into something meaningful, i.e. turn data into ciphertext. A key is typically used to perform the encryption’s numeric calculation and the same key is used to decrypt the encrypted data. One way of achieving this is by using a XOR cipher; XOR (exclusive or) is an operation that works like OR but returns zero when both conditions are true.
0 XOR 0 = 0
1 XOR 1 = 0
1 XOR 0 = 1
0 XOR 1 = 1If our data (in binary) is 00110011 and our key is 11110000 then:
data = 00110011
key = 11110000
ciphertext = 11000011If we use the same key on the ciphertext, we obtain the original data:
ciphertext = 11000011
key = 11110000
data = 00110011A hash function converts data into a random string of fixed length. The MD5 message-digest algorithm is a widely used (but outdated) hash function that produces a 128-bit hash value.
echo hello world | md56f5902ac237024bdd0c176cb93063dc4The output is in hexadecimal (0-9 then A-F), which requires 4 bits to represent because F in hexadecimal is 1111 in binary. Therefore the 32 long hexadecimal number is 32*4 bits. Any data used as input into the MD5 hash function will return a 128-bit hash value or a length 32 hexadecimal number.
echo abc | md50bee89b07a248e27c83fc3d5951213c1When given the same input, a hash function will invariably produce the same output.
echo hello world | md56f5902ac237024bdd0c176cb93063dc4However, if the input data only differs by a single bit, the output is very different.
echo hell world | md5a3723e12600ef5c0456c201f5e8c7a37Sometimes, completely different data can produce identical hash values but this has a very low probability and is known as a hash collision. Finally, it is impossible to convert hash values back into their original data.