Last updated: 2023-06-27

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Knit directory: bioinformatics_tips/

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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 e4ad29d Dave Tang 2023-06-27 Update jquery
html c6a497c davetang 2020-06-21 Build site.
Rmd 3b81b96 davetang 2020-06-21 Queuing systems
html 02c559c davetang 2020-06-08 Build site.
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:

  1. Interception
  2. Spoofing
  3. Falsification
  4. Repudication

These four problems are countered by:

  1. Encryption
  2. Message authenitcation codes (MACs) or digital signatures
  3. MACs or digital signatures
  4. Digital signatures and certificates

Encryption

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.

If our data (in binary) is 00110011 and our key is 11110000 then:

If we use the same key on the ciphertext, we obtain the original data:

Hash functions

A 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 The MD5 message-digest algorithm is a widely used (but outdated) hash function that produces a 128-bit hash value.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 | md5sum
6f5902ac237024bdd0c176cb93063dc4  -

The 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 | md5sum
0bee89b07a248e27c83fc3d5951213c1  -

When given the same input, a hash function will invariably produce the same output.

echo hello world | md5sum
6f5902ac237024bdd0c176cb93063dc4  -

However, if the input data only differs by a single bit, the output is very different.

echo hell world | md5sum
a3723e12600ef5c0456c201f5e8c7a37  -

Sometimes, 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.

Shared-key cryptosystem

Shared-key or symmetric-key cryptosystems use the same key for encryption and decryption. The Advanced Encryption Standard is the first (and only) publicly accessible cipher approved by the National Security Agency (NSA).

The problem with shared-key systems is that in order for the receiving party to decrypt the encrypted file, the key needs to be transferred as well. A secure method is necessary for transmitting keys, i.e. performing a key-exchange. There are two types of methods:

  1. Methods using key-exchange protocols
  2. Methods using the public-key cryptosystem

Public-key cryptosystem

Unlike the shared-key cryptosystem, the public-key cryptosystem uses different keys for encryption and decryption.

To be continued…


sessionInfo()
R version 4.3.0 (2023-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.2 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: Etc/UTC
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] workflowr_1.7.0

loaded via a namespace (and not attached):
 [1] vctrs_0.6.3      httr_1.4.5       cli_3.6.1        knitr_1.42      
 [5] rlang_1.1.1      xfun_0.39        stringi_1.7.12   processx_3.8.1  
 [9] promises_1.2.0.1 jsonlite_1.8.4   glue_1.6.2       rprojroot_2.0.3 
[13] git2r_0.32.0     htmltools_0.5.5  httpuv_1.6.9     ps_1.7.5        
[17] sass_0.4.5       fansi_1.0.4      rmarkdown_2.21   jquerylib_0.1.4 
[21] tibble_3.2.1     evaluate_0.20    fastmap_1.1.1    yaml_2.3.7      
[25] lifecycle_1.0.3  whisker_0.4.1    stringr_1.5.0    compiler_4.3.0  
[29] fs_1.6.2         pkgconfig_2.0.3  Rcpp_1.0.10      rstudioapi_0.14 
[33] later_1.3.0      digest_0.6.31    R6_2.5.1         utf8_1.2.3      
[37] pillar_1.9.0     callr_3.7.3      magrittr_2.0.3   bslib_0.4.2     
[41] tools_4.3.0      cachem_1.0.7     getPass_0.2-2