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

Address of the bookmark: https://github.com/marbl/Krona/wiki

1. Learn and get updated

Some of the bad biological programmers only learn new technical or non-technical things when it’s absolutely necessary. The good biological programmers learn new technical skills proactively. But great biological programmers not only learn new technical skills on their own but also learn non-technical skills, and have an open mind to sources of knowledge that others may shut out.

In other concrete term, the bad biological programmer learn Perl's regular expression when they started a project on comparative genomics; the good biological programmer learned it a year before because it looked interesting; and the great biological programmer also read about the BioPerl packages, genomics, DNA string, genomic theories, or some similar course of study so that they could understand the results and explain it biologically.

2. Not a merely coder!!!

I often encountered with biological programmer who call themself a hard-core computer programmer and avoid biology. I can almost guarantee that if you are one of them then you are not doing research but merely writing "dry" codes.

According to my supervisor most of the computational biologist, don't know what they are doing biologically. Even they struggle to explain their own programs output and results. Therefore, It is highly advisable to learn basic of biology which can assist you to explain the result and understand your discovery. Always remember you are a researcher not a coder.

3. Be Social with biologist

The computational biologist spends most of the time in from of computers, writing codes. They always think their job is to produce working codes, not technical research perfections. But, they are completely wrong. You should not forget that apart from your computational skills you also need some biologist, other than your supervisor, to explain and make you understand the complex biological mechanism.

I highly recommend your to interact with biotech researchers and learn how do they explain their one graph (which they generally produce after one year of work) biologically. Remember, the origin of your research project is complex biological phenomenon, which is more complex than that of your limited programming rules.

4. Do not search, research for answers

Researching for answers means more than typing several keywords into a search engine or posting a question at Stack Overflow or the BioStars forums. I have entered problems into search engines that generate no results, and every question I posted on Stack Overflow or the BioStars forums never got anything resembling an answer, yet I solved the issues and moved on. I’m not a magician — I just know how to find answers or discover root causes.

Many problems are situational, and if you depend on search engines and forums, you can waste a lot of time going down a rabbit hole and possibly never getting a solution. Learn to perform root cause analysis, learn enough about the underlying system to look for other clues and solutions, and learn to take a long distance view of an issue before deep diving into it.

5. Love and defend your research

You cannot rise to the top in this research profession without loving your work. There are some very good “it’s just a job” biological programmers (I’ve been one at times), but if that is your outlook, you won’t be willing to do whatever it takes to succeed. This idea gets a lot of folks in a huff, because they feel it is a personal insult. “I’m a good programmer, but I have other priorities and can’t make work my life.” I understand completely; I have other priorities too. As much as I hate to say it, when I am passionate about my work, I am willing (though not eager) to abandon my other priorities to finish the job. It is not an insult to say that if you aren’t willing to pull out all the stops you can’t be the best, it is a fact.

You must be passionate about more than programming — you must also be excited about your research, the tools and technology you are using, and so on. I have seen very good and even great biological programmers operating at mediocre levels because something was not a good fit, such as they hated the project or were using a technology they disliked. Therefore, like your research project and get excited about your discoveries. You have not only to discover but also defend your finding with scientific words.

Thanks to all of you for reading.

Address of the bookmark: http://denbi-metagenomics-workshop.readthedocs.io/en/latest/index.html

MEME Suite software development; gene expression; mathematical modelling; gene regulation and transcription

Specialization:
Pattern recognition and modelling in computational biology

Link @ http://www.imb.uq.edu.au/tim-bailey

It was originally developed at the Wellcome Trust Sanger Institute to bundle a FASTA sequence and its quality data, but has recently become the de facto standard for storing the output of high-throughput sequencing instruments such as the Illumina Genome Analyzer.^[1]

Address of the bookmark: https://en.wikipedia.org/wiki/FASTQ_format

Applications are invited for the STUDENTSHIP and TRAINEESHIP vacancies to carry out project/research work in the DBT - Bioinformatics Infrastructure Facility with consolidated stipend of Rs.5,000/- per month.

Essential Qualification

Student Trainee: Those who have completed M.Sc., Bioinformatics/Biophysics/Life sciences or Pursuing M.Tech., Bioinformatics/Biotechnology

Duration : 3-4 Months

Student Trainee: Those who are pursuing M.Sc Bioinformatics/Biophysics/ Life sciences/others

Duration : 2-3 Months

Mail your CV on or before 25th November 2013 to shirai2011@gmail.com and hard copy to "Dr. D. Velmurugan, Professor & Head, CAS in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025". Also, the applicants are requested to attend the interview on 29th November, 2013 at 11 A.M.

Advertisement:

www.unom.ac.in/uploads/announcements/bifadvertisement_20131114080003_23240.pdf

Today, refreshing my old memories I decided to blog about the basic knowledge of biochemistry and computational proteomics skills, but after I found several article on internet saying exactly what I had wanted to say I thought I might as well just redirect BOL's blog readers there instead:

Here is the list of website and videos links which provide a good resource for you basic chemistry need:

http://tecreativ.blogspot.co.uk/2012/09/funny-shortcut-remember-periodic-table.html

This blog have some specific hindi word to remember entire periodic table. I really like

Group 14 (C Si Ge Sn Pb) -> Sentence “Chemistry Sir Gives Sanki Problems”

Sanki is a hindi word which mean crazy :P

I found this link useful as well http://www.wikihow.com/Memorise-the-Periodic-Table

The eagle genomics group provide an element of bioinformatics in periodic tables. Yes you got it, this is not periodic table rather bioinformatics tools with periodicals

http://elements.eaglegenomics.com/

You can also try this video links, which provide you an overview with tricks on periodic tables:

http://www.youtube.com/watch?v=fLSfgNxoVGk

http://www.youtube.com/user/periodicvideos

For drug design educational material, software, tools, databses, viewer, file format and many more stuff at one place http://www.allfordrugs.com/drug-design/ I highly recommend you all computational drug designer to bookmark this page for future studies as well.

I just remember one of my mini project in which I use my flash knowledge (flash .. oh ya flash) to explain amino acids in interactive and user friendly manner. I can’t provide It right now, but promise you to provide a link in near future. I hope that you will enjoy my flashy creative skills :).

Moreover, I found some of very interesting tricks to remember all amino acids chemical formulae on youtube at

http://www.youtube.com/watch?v=gqrWb0fmzQ&list=PL6132651E70BB5575

http://www.youtube.com/watch?v=C2GfoGXfySQ&list=PL6132651E70BB5575

Key points for computer added drug designers?
1. A shortage of biochemistry skills means that you absolutely nowhere in understanding the key concept and do research.
2. Keep handy with complex mathematical formula, before merely running tools or software.
3. Dig it better and deeper guys .. design it.

Courses

Old courses (2012-2014)

Metagenomics Workshop

2015 November - Uppsala
2016 November - Uppsala
2017 November - Uppsala

Introduction to Bioinformatics Using NGS Data

2015 February - Uppsala 
2015 May - Gothenburg
2015 September - Uppsala
2015 November - Lund
2016 January - Uppsala
2016 April - Linköping
2016 September - Uppsala
2016 November - Umeå
2017 January - Uppsala
2017 May - Gothenburg
2017 September - Lund
2017 November - Uppsala
2018 February - Uppsala

Introduction to Genome Annotation

2015 April - Uppsala
2016 April - Uppsala
2017 April - Uppsala
2018 May - Uppsala

De Novo Genome Assembly

2016 November - Uppsala
2017 November - Uppsala

RNA-seq course

2015 October - Uppsala
2016 April - Uppsala
2016 October - Uppsala
2017 March - Uppsala
2017 November - Uppsala
RNAseq tutorials

R Programming Foundations for Life Scientists

2016 November - Uppsala
2017 Mars - Uppsala

Single cell RNA sequencing analysis

2017 October - Uppsala

Address of the bookmark: https://scilifelab.github.io/courses/