More at http://gkno.me/

Address of the bookmark: http://gkno.me/

In C, "sequence statements" are imperatives. The "selection" is the "if then else" statement, and the iteration is satisfied by a number of statements, such as the "while," " do," and the "for," while the case-type statement is satisfied by the "switch" statement.

Pseudocode is an artificial and informal language that helps programmers develop algorithms. Pseudocode is a "text-based" detail (algorithmic) design tool.

The rules of Pseudocode are reasonably straightforward. All statements showing "dependency" are to be indented. These include while, do, for, if, switch. Examples below will illustrate this notion.

GUIDE TO PSEUDOCODE LEVEL OF DETAIL: Given record/file descriptions, pseudocode should be created in sufficient detail so as to directly support the programming effort. It is the purpose of pseudocode to elaborate on the algorithmic detail and not just cite an abstraction.

Examples:

1.

If student's grade is greater than or equal to 60
    Print "passed"
else
    Print "failed"  
endif

2.

  
Set total to zero
Set grade counter to one
While grade counter is less than or equal to ten
    Input the next grade
    Add the grade into the total
endwhile 
Set the class average to the total divided by ten
Print the class average.

3.

Initialize total to zero
Initialize counter to zero
Input the first grade
while the user has not as yet entered the sentinel
   add this grade into the running total 
   add one to the grade counter  
   input the next grade (possibly the sentinel)
endwhile

if the counter is not equal to zero
   set the average to the total divided by the counter
   print the average  
else
   print 'no grades were entered' 
endif 

4.

initialize passes to zero
initialize failures to zero
initialize student to one
while student counter is less than or equal to ten
    input the next exam result  
    if the student passed

add one to passes else add one to failures add one to student counter endif endwhile print the number of passes print the number of failures if eight or more students passed print "raise tuition" endif

5.

Larger example:  

NOTE:  NEVER ANY DATA DECLARATIONS IN PSEUDOCODE

Print out appropriate heading and make it pretty
While not EOF do:
     Scan over blanks and white space until a char is found 
	(get first character on the line)
     set can't-be-ascending-flag to 0
     set consec cntr to 1
     set ascending cntr to 1
     putchar first char of string to screen
     set read character to hold character
     While next character read != blanks and white space
          putchar out on screen
          if new char = hold char + 1
               add 1 to consec cntr
               set hold char = new char
               continue
          endif
          if new char >= hold char 
               if consec cntr < 3 
                    set consec cntr to 1
               endif
               set hold char = new char
               continue
          endif
          if new char < hold char
               if consec cntr < 3
                    set consec cntr to 1
               endif
               set hold char = new char
               set can't be ascending flag to 1
               continue
           endif
     end while
     if consec cntr >= 3 
          printf (Appropriate message 1 and skip a line)
          add 1 to consec total
     endif
     if  can't be ascending flag = 0
          printf (Appropriate message 2 and skip a line)
          add 1 to ascending total
     else
          printf (Sorry message and skip a line)
          add 1 to sorry total
     endif
end While
Print out totals:  Number of consecs, ascendings, and sorries.
Stop

Some Keywords That Should be Used And Additional Points

For looping and selection, The keywords that are to be used include Do While...EndDo; Do Until...Enddo; While .... Endwhile is acceptable. Also, Loop .... endloop is also VERY good and is language independent. Case...EndCase; If...Endif; Call ... with (parameters); Call; Return ....; Return; When;

Always use scope terminators for loops and iteration.

As verbs, use the words Generate, Compute, Process, etc. Words such as set, reset, increment, compute, calculate, add, sum, multiply, ... print, display, input, output, edit, test , etc. with careful indentation tend to foster desirable pseudocode. Also, using words such as Set and Initialize, when assigning values to variables is also desirable.

More on Formatting and Conventions in Pseudocoding

• INDENTATION in pseudocode should be identical to its implementation in a programming language. Try to indent at least four spaces.
• As noted above, the pseudocode entries are to be cryptic, AND SHOULD NOT BE PROSE. NO SENTENCES.
• No flower boxes (discussed ahead) in your pseudocode.
• Do not include data declarations in your pseudocode.
• But do cite variables that are initialized as part of their declarations. E.g. "initialize count to zero" is a good entry.

  ---

  Function Calls, Function Documentation, and Pseudocode
• Calls to Functions should appear as:
• Returns in functions should appear as:
• Function headers should appear as:
• Note that in C, arguments and parameters such as "fieldn" could be written: "pointer to fieldn ...."
• Functions called with addresses should be written as:
• Function headers containing pointers should be indicated as:
• Returns in functions where a pointer is returned:
• It would not hurt the appearance of your pseudocode to draw a line or make your function header line "bold" in your pseudocode. Try to set off your functions.
• Try to use scope terminators in your pseudocode and source code too. It really hels the readability of the text.

  ---

  Source Code
• EVERY function should have a flowerbox PRECEDING IT. This flower box is to include the functions name, the main purpose of the function, parameters it is expecting (number and type), and the type of the data it returns. All of these listed items are to be on separate lines with spaces in between each explanatory item.
• FORMAT of flowerbox should be

   

  	 ********************************************************
  	 Function:   ( cryptic text describing single function
  		     ....... (indented like this) 	
  		     .......
  	 Calls:      Start listing functions "this" function calls
  		     Show these functions:  one per line, indented
  
  	 Called by:  List of functions that calls "this" function
  		     Show these functions:  one per line, indented.
  
  	 Input Parameters:  list, if appropriate; else None
  	 
  	 Returns:    List, if appropriate.
  	 ****************************************************************
  

• INDENTATION is critically important in Source Code. Follow standard examples given in class. If in doubt, ASK. Always indent statements within IFs, FOR loops, WILLE loops, SWITCH statements, etc. a consistent number of spaces, such as four. Alternatively, use the tab key. One or two spaces is insufficient.
• Use scope terminators at the end of if statements, for statements, while statements, and at the end of functions. It will make your program much more readable.

  SPELLING ERRORS ARE NOT ACCEPTABLE

CORE MODULES

Three modules make up the core engine for MCE.

MCE::Core

Provides the Core API for Many-Core Engine. The various MCE options are described here.

MCE::Signal

Temporary directory creation, cleanup, and signal handling.

MCE::Util

Utility functions for Many-Core Engine.

MCE EXTRAS

There are 4 add-on modules for use with MCE.

MCE::Candy

Provides a collection of sugar methods and output iterators for preserving output order.

MCE::Mutex

Provides a simple semaphore implementation supporting threads and processes.

MCE::Queue

Provides a hybrid queuing implementation for MCE supporting normal queues and priority queues from a single module. MCE::Queue exchanges data via the core engine to enable queuing to work for both children (spawned from fork) and threads.

MCE::Relay

Enables workers to receive and pass on information orderly with zero involvement by the manager process while running.

MCE MODELS

The models take Many-Core Engine to a new level for ease of use. Two options (chunk_size and max_workers) are configured automatically as well as spawning and shutdown.

MCE::Loop

Provides a parallel loop utilizing MCE for building creative loops.

MCE::Flow

A parallel flow model for building creative applications. This makes use of user_tasks in MCE. The author has full control when utilizing this model. MCE::Flow is similar to MCE::Loop, but allows for multiple code blocks to run in parallel with a slight change to syntax.

MCE::Grep

Provides a parallel grep implementation similar to the native grep function.

MCE::Map

Provides a parallel map model similar to the native map function.

MCE::Step

Provides a parallel step implementation utilizing MCE::Queue between user tasks. MCE::Step is a spin off from MCE::Flow with a touch of MCE::Stream. This model, introduced in 1.506, allows one to pass data from one sub-task into the next transparently.

MCE::Stream

Provides an efficient parallel implementation for chaining multiple maps and greps together through user_tasks and MCE::Queue. Like with MCE::Flow, MCE::Stream can run multiple code blocks in parallel with a slight change to syntax from MCE::Map and MCE::Grep.

MISCELLANEOUS

Miscellaneous additions included with the distribution.

MCE::Examples

Describes various demonstrations for MCE including a Monte Carlo simulation.

MCE::Subs

Exports functions mapped directly to MCE methods; e.g. mce_wid. The module allows 3 options; :manager, :worker, and :getter.

REQUIREMENTS

Perl 5.8.0 or later. PDL::IO::Storable is required in scripts running PDL.

SOURCE AND FURTHER READING

The source, cookbook, and examples are hosted at GitHub.

• https://github.com/marioroy/mce-perl

• https://github.com/marioroy/mce-cookbook

• https://github.com/marioroy/mce-examples

SEE ALSO

MCE::Shared provides data sharing capabilities for MCE. It includes MCE::Hobo for running code asynchronously.

• MCE::Shared

• MCE::Hobo

Address of the bookmark: https://github.com/marioroy/mce-examples

Training Resources:

• Bioinformatics Workshop (Webinars)
• Bioinformatics Training Slides

Specialized Applications:

• De Novo Assembly
• Transcriptome analysis
• Base Modification Analysis
• Barcoding
• Data Analysis Tools
• Minor Variants and Phasing Analysis

Address of the bookmark: https://github.com/PacificBiosciences/Bioinformatics-Training/wiki

Here is how I use the blasr to align PacBio reads to the contigs (target.fasta). The “target.fasta.sa” is the suffix array from “target.fasta” generated by sawriter.

blasr query.fa ./target.fasta -sa ./target.fasta.sa -bestn 40 -maxScore -500 -m 4 -nproc 24 -out target.m4 -maxLCPLength 15

the output format option “-m 4″ generate the alignment coordinate. Not fully documented, but I can explain that to you. 

I use a 24 cores / 48G ram server for the alignment. It took about 2 to 3 hours aligning 3G PacBio Reads to 10^6 sequences of short read contigs with a mean 3.5kbp length.

Address of the bookmark: http://bix.ucsd.edu/projects/blasr/

• Bioinformatics - RSS feed of current and advance online publications
• Genome Research - current & advance
• Genome Biology - editors picks, latest, most viewed, most forwarded. (Hit the RSS icon under each tab).
• PLoS Genetics - new articles
• PLoS Computational Biology - new articles
• Nature Genetics - current TOC and AOP
• Nature Reviews Genetics - current TOC and AOP

• Bioinformatics
• BMC Bioinformatics
• Briefings in Bioinformatics
• Genome Biology
• Genome Research: current and AOP
• Microbiome
• Nature Genetics, current & AOP
• Nature Reviews Genetics, current & AOP
• Nucleic Acids Research
• PLOS Computational Biology
• PLOS Genetics

Blogs. Some of these blogs are very relevant to bioinfo jobs. Others are more personal interest.

• The OpenHelix Blog
• Ensembl blog
• Galaxy News
• Blue Collar Bioinformatics
• Homologus
• Golden Helix - our 2 SNPs
• Genomics Law Report
• R-bloggers (aggregates feeds from >350 blogs about R)
• Genomes Unzipped
• Jason Moore's Epistasis Blog
• 23andMe - the Spitoon

• Variance Explained: David Robinson’s blog (Data Scientist at Stack Overflow, works in R and Python).
• Global Biodefense: News on pathogens, outbreaks, and preparedness, with periodic posts on genomics and bioinformatics-related developments and funding opportunities.
• In between lines of code: Lex Nederbragt’s blog on biology, sequencing, bioinformatics, …
• Simply Statistics: A statistics blog by Rafa Irizarry, Roger Peng, and Jeff Leek.
• Bits of DNA: Reviews and commentary on computational biology by Lior Pachter (fair warning: dialogue here can get a bit heated!).
• Blue Collar Bioinformatics: articles related tool validation and the open source bioinformatics community.
• Microbiome Digest – Bik’s Picks: A daily digest of scientific microbiome papers, by Elisabeth Bik, Science Editor at uBiome.
• Living in an Ivory Basement: Titus Brown’s blog on metagenomics, open science, testing, reproducibility, and programming.
• Enseqlopedia: James Hadfield’s blog on all things NGS.
• Epistasis Blog: Jason Moore’s computational biology blog.
• RStudio Blog: announcements about new RStudio functionality, updates about the tidyverse, and more.
• nextgenseek.com: Next-Gen Sequencing Blog covering new developments in NGS data & analysis.
• RNA-Seq Blog: Transcriptome Research & Industry News.
• The Allium: We all need a little humor in our lives. Like The Onion, but for science.

Forums.

• Seqanswers - bioinformatics forum
• Seqanswers - RNA-Seq forum
• BioStar
• BOL

Address of the bookmark: https://github.com/baoxingsong/AnchorWave

Project Title : “Integrating genome scale metabolic analysis of model plant pathogen Ralstonia solanacearum with RNAseq and fluxomics”

Essential qualification : M.Tech. in CSE/IT (With specialization in Computational Biology/Bioinformatics) or M.Sc. in Bioinformatics/Biosciences/Molecular Biology Biotechnology preferably with NET/GATE/BET. Candidates should have minimum 55 % mark both in 10th and 10+2 Science examinations and mathematics at 10+2 Science. Desirable: Preference will be given to the candidates having experience in computational analysis of genome sequences or similar projects.

No. of Post : 01

Remuneration : Rs. 25,000/- for the 1st two years and Rs. 28,000/- for the 3rd year for SRF and applicable to the candidate having post graduate degree in Basic Science with NET/GATE/BET qualification or post graduate degree in professional course. Rs. 12,000/- for the 1st two years and Rs. 14,000/- for the 3 rd year for SRF,

Age : 28 years

Duration : Three (03) years or till completion of the project or until further order, whichever is earlier.

Hiring Process : Walk - In
Job Role: Research/JRF/SRF

Walk-in-interview will be held on 17th February, 2017, 11.15 a.m. at the office of the Head, Department of Computer Science and Engineering, Tezpur University.

Interested candidates may appear before the interview board with original documents from 10th standard onwards and photocopies of mark sheets, certificates, testimonials, caste certificate (if applicable), experience certificate certificates of NET/GATE/BET or similar examination qualifications, any other testimonials and a copy of recent curriculum vitae (CV) on the day of interview.

More at http://www.tezu.ernet.in/ProjectWalkin/Advt-DoRD-CSE-SSS-20-295-112-A.pdf

Searcg link https://metagraph.ethz.ch/search 

Pre-print https://www.biorxiv.org/content/10.1101/2020.10.01.322164v4 

Address of the bookmark: https://metagraph.ethz.ch/