BOL: Related items

Cheatsheet for Linux !!

Jit — Wed, 22 Jun 2016 07:55:06 -0500

Linux Commands Cheat Sheet

    File System

    ls — list items in current directory

    ls -l — list items in current directory and show in long format to see perimissions, size, an modification date

    ls -a — list all items in current directory, including hidden files

    ls -F — list all items in current directory and show directories with a slash and executables with a star

    ls dir — list all items in directory dir

    cd dir — change directory to dir

    cd .. — go up one directory

    cd / — go to the root directory

    cd ~ — go to to your home directory

    cd - — go to the last directory you were just in

    pwd — show present working directory

    mkdir dir — make directory dir

    rm file — remove file

    rm -r dir — remove directory dir recursively

    cp file1 file2 — copy file1 to file2

    cp -r dir1 dir2 — copy directory dir1 to dir2 recursively

    mv file1 file2 — move (rename) file1 to file2

    ln -s file link — create symbolic link to file

    touch file — create or update file

    cat file — output the contents of file

    less file — view file with page navigation

    head file — output the first 10 lines of file

    tail file — output the last 10 lines of file

    tail -f file — output the contents of file as it grows, starting with the last 10 lines

    vim file — edit file

    alias name 'command' — create an alias for a command
    System

    shutdown — shut down machine

    reboot — restart machine

    date — show the current date and time

    whoami — who you are logged in as

    finger user — display information about user

    man command — show the manual for command

    df — show disk usage

    du — show directory space usage

    free — show memory and swap usage

    whereis app — show possible locations of app

    which app — show which app will be run by default
    Process Management

    ps — display your currently active processes

    top — display all running processes

    kill pid — kill process id pid

    kill -9 pid — force kill process id pid
    Permissions

    ls -l — list items in current directory and show permissions

    chmod ugo file — change permissions of file to ugo - u is the user's permissions, g is the group's permissions, and o is everyone else's permissions. The values of u, g, and o can be any number between 0 and 7.

    7 — full permissions

    6 — read and write only

    5 — read and execute only

    4 — read only

    3 — write and execute only

    2 — write only

    1 — execute only

    0 — no permissions

    chmod 600 file — you can read and write - good for files

    chmod 700 file — you can read, write, and execute - good for scripts

    chmod 644 file — you can read and write, and everyone else can only read - good for web pages

    chmod 755 file — you can read, write, and execute, and everyone else can read and execute - good for programs that you want to share
    Networking

    wget file — download a file

    curl file — download a file

    scp user@host:file dir — secure copy a file from remote server to the dir directory on your machine

    scp file user@host:dir — secure copy a file from your machine to the dir directory on a remote server

    scp -r user@host:dir dir — secure copy the directory dir from remote server to the directory dir on your machine

    ssh user@host — connect to host as user

    ssh -p port user@host — connect to host on port as user

    ssh-copy-id user@host — add your key to host for user to enable a keyed or passwordless login

    ping host — ping host and output results

    whois domain — get information for domain

    dig domain — get DNS information for domain

    dig -x host — reverse lookup host

    lsof -i tcp:1337 — list all processes running on port 1337
    Searching

    grep pattern files — search for pattern in files

    grep -r pattern dir — search recursively for pattern in dir

    grep -rn pattern dir — search recursively for pattern in dir and show the line number found

    grep -r pattern dir --include='*.ext — search recursively for pattern in dir and only search in files with .ext extension

    command | grep pattern — search for pattern in the output of command

    find file — find all instances of file in real system

    locate file — find all instances of file using indexed database built from the updatedb command. Much faster than find

    sed -i 's/day/night/g' file — find all occurrences of day in a file and replace them with night - s means substitude and g means global - sed also supports regular expressions
    Compression

    tar cf file.tar files — create a tar named file.tar containing files

    tar xf file.tar — extract the files from file.tar

    tar czf file.tar.gz files — create a tar with Gzip compression

    tar xzf file.tar.gz — extract a tar using Gzip

    gzip file — compresses file and renames it to file.gz

    gzip -d file.gz — decompresses file.gz back to file
    Shortcuts

    ctrl+a — move cursor to beginning of line

    ctrl+f — move cursor to end of line

    alt+f — move cursor forward 1 word

    alt+b — move cursor backward 1 word

Machine Learning !!!

Gudiya Pal — Fri, 01 Jul 2016 12:57:12 -0500

In machine learning, computers apply statistical learning techniques to automatically identify patterns in data. These techniques can be used to make highly accurate predictions.

Keep scrolling. Using a data set about homes, we will create a machine learning model to distinguish homes in New York from homes in San Francisco.

Address of the bookmark: http://www.r2d3.us/visual-intro-to-machine-learning-part-1/

BINC exam preparation tips !!

Jit — Fri, 15 Jul 2016 20:53:01 -0500

How to prepare for BINC (BioInformatics National Certification) exam? What are the expected questions?

These are just a scant few of the common questions asked by bioinformatics students as they ready themselves for the next exam sitting. If you read the entire Syllabus (and I know that everyone does), you will see a section devoted to study and exam techniques. The section discusses such broad concepts as motivation, scheduling, and retention. Upon reading this section, however, I find the "hints" to be too general. Much of the advice boils down to read, study, understand, and memorize the material. The techniques mentioned apply to everyone and thus the overall advice ends up as a broad overview of the learning process.

The idea behind this article is to give students ideas on different approaches and techniques in the preparation for exams. By providing various ways to prepare for the exam process, fascinated readers may gain some additional insight to help complement their studying methodology. There are, of course, many common themes expressed in this small empirical sample of students' study habits. The idea of note cards, memorization, and problem solving are frequently mentioned by all students. No matter what technique a candidate uses, it always takes a significant amount of time and personal resources to successfully complete the examination process.

1 Explain it in your own word

Your teacher or lecturer can explain something to you, you can learn it from a text book, your friends can study with you, even your own notes can explain it to you but all these explanations are of little use if, by the end, you can’t explain what you have learned to yourself. The BINC exam looking for ability to write and explain the concept in your own word. You, therefore, need to illustrate in an exam to get top exam results, then you won’t be happy with your end exam result. So don’t just memorise and tick off the list – make sure you understand your theory.

2 Be an examiner yourself

Of course, depending on what you’re studying, it may be quite difficult to get into a position to understand a concept, theory or other information you need to learn. Ask ‘stupid’ question to yourself and train yourself for the worst! Embrace your curiosity, for as William Arthur Ward said: “Curiosity is the wick in the candle of learning.” Doing so will allow you to fill in the blanks and better prepare you for exams.

3 Quiz yourself

Once you feel you understand topic, it is important to test yourself regularly. Try yourself to replicate exam conditions as much as possible: turn your phone off, don’t talk, time yourself etc. You can set yourself a study quiz or practice exam questions and, so long as you approach it with the right mindset, you can get a very good idea of how much you know. You gain a greater insight into where you stand in relation to what you’ve studied so far.

4 Online study

Keeping the fact that, bioinformatics is ever changing subject, you might need to update yourself on timely basis. Don’t feel obliged to just sit in front of a book with a highlighter; there are many different ways to improve your bioinformatics knowledge. Login and check almost all web servers and keep yourself updated, like how many genomes sequenced, sizes, techniques used, software names etc.

5 Study plan

In order to achieve exam success, you need to know what you want to achieve and focus on. That’s why it is extremely important to set your Study Goals now and outline to yourself what you need to do. With your study goals in mind, you properly need to attention all subjects. It should be broad enough to allow you to add and change aspects but concise enough so you know you’re covering each subject/topic as best you can at this point.

Bioinformatics Scientist – ICMR Computational Genomics Centre

Sat, 26 Dec 2020 10:18:29 -0600

ICMR invites online applications, from Indian Citizens, up to 8th January 2020 till 5:30 PM to fill up the following post to be filled purely on a temporary basis under “ICMR Computational Genomics Centre” under Dr. Harpreet Singh, Head, Division of Biomedical Informatics (BMI), ICMR HQRS, New Delhi 110029.
The Terms & Conditions for the post are as follows:

a) Scientist-B – UR (2 posts-Bioinformatics) on consolidated salary of Rs.48,000/- pm + HRA

b) Scientist C – UR (1 post -Bioinformatics) on consolidated salary of Rs. 51,000 pm+ HRA

c) Scientist B- UR (2 post-Statistics) on a consolidated salary of Rs.48,000/- pm +HRA

d) Computer Programmer 1 post UR & 1 post SC on a consolidated salary of Rs. 32,500/- pm

e) Research Assistant -UR 1 post on a consolidated salary of Rs. 31,000/- pm

More at https://projectjobs.icmr.org.in/sccbioinformatics/uploads/recruitment/Adv_BMI_24122020.pdf

CGView - Circular Genome Viewer

Jit — Mon, 19 Sep 2016 07:52:26 -0500

GView is a Java package used to display and navigate bacterial genomes. GView is useful for producing high-quality genome maps for use in publications and websites, or as a visualization tool in a sequence annotation pipeline. Users can interact with the genome using a powerful pan-and-zoom interface, or GView can write static images of a genome to a file. GView can draw a genome using either circular or linear layouts. For examples of some of the images GView can produce, see the Image Gallery. GView is a re-write of CGView, a circular genome viewer written by Paul Stothard. The goal of GView is to provide greater user interaction, and more flexibility in how the genome map is rendered. To aid with easily configuring the display of a genome, a style editor has been included to provide an intuitive, user-friendly graphical user interface for customizing genome maps. Styling attributes such as colours or fonts for the various map elements can be adjusted in real time. Customized styles can be saved for later use or for application to other genome maps using GView's custom file format.

Address of the bookmark: http://wishart.biology.ualberta.ca/cgview/

BLAST Ring Image Generator (BRIG)

Anjana — Fri, 30 Sep 2016 09:18:50 -0500

BRIG is a free cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data. The application is available at: http://sourceforge.net/projects/brig

If you have any questions or comments, post them on one of the trackers on BRIG’s SourceForge page: http://sourceforge.net/tracker/?group_id=328245.

Features:

Images show similarity between a central reference sequence and other sequences as concentric rings.
BRIG will perform all BLAST comparisons and file parsing automatically via a simple GUI.
Contig boundaries and read coverage can be displayed for draft genomes; customized graphs and annotations can be displayed.
Using a user-defined set of genes as input, BRIG can display gene presence, absence, truncation or sequence variation in a set of complete genomes, draft genomes or even raw, unassembled sequence data.
BRIG also accepts SAM-formatted read-mapping files enabling genomic regions present in unassembled sequence data from multiple samples to be compared simultaneously

Address of the bookmark: http://brig.sourceforge.net/

How to install Perl modules on Mac OS X in easy steps !!

Jit — Thu, 20 Oct 2016 07:26:29 -0500

Today at work, I learned how to install Perl modules using CPAN. It’s a lot easier than I thought.

You see, for the past couple of years, I’ve been a bit frustrated because OS X does not come with a whole lot of Perl modules pre-installed, and for all I googled, I couldn’t find an “idiot’s” guide for moderately-savvy-but-not-expert users like myself to install modules and dependencies on demand.

The only instructions I could find point to Fink, which basically installs modules in a path that isn’t included in the Perl @INC variable, meaning you have to manually specify the full path to the modules in every script — which is not a lot of fun if you’re developing on OS X and deploying on Red Hat, for instance.

Moreover, Fink doesn’t seem to make every module available, and it’s not very easy to determine which Fink package you need to install if you need a particular module.

So, with a script that called on several apparently unavailable modules, and a deadline looming, I finally decided to suck it up and figure out how to use CPAN to install them:

1) Make sure you have the Apple Developer Tools (XCode) installed.

These are on one of your install discs, or available as a huge but free download from the Apple Developer Connection [free registration required] or the Mac App Store. I thought I had them, but apparently when we upgraded that computer to Tiger, they went missing.

If you don’t have this stuff installed, your installation will fail with errors about unavailable commands.

1.5) Install Command Line Tools (Recent XCode versions only)

(Thank you to Tom Marchioro for informing me about this step.)

Older versions of XCode installed the command line tools (which are required to properly install CPAN modules) by default, but apparently newer ones do not. To check whether you have the command line tools already installed, run the following from the Terminal:

$ which make

This command checks the system for the “make” tool. If it spits out something like /usr/bin/make you’re golden and can skip ahead to Step 2. If you just get a new prompt and no output, you’ll need to install the tools:

Launch XCode and bring up the Preferences panel.
Click on the Downloads tab
Click to install the Command Line Tools

If you like, you can run which make again to confirm that everything’s installed correctly.

2) Configure CPAN.

$ sudo perl -MCPAN -e shell

perl> o conf init

This will prompt you for some settings. You can accept the defaults for almost everything (just hit “return”). The two things you must fill in are the path to make (which should be /usr/bin/make or the value returned when you run which make from the command line) and your choice of CPAN mirrors (which you actually choose don’t really matter, but it won’t let you finish until you select at least one). If you use a proxy or a very restrictive firewall, you may have to configure those settings as well.

If you skip Step 2, you may get errors about make being unavailable.

3) Upgrade CPAN

$ sudo perl -MCPAN -e 'install Bundle::CPAN'

Don’t forget the sudo, or it’ll fail with permissions errors, probably when doing something relatively unimportant like installing man files.

This will spend a long time downloading, testing, and compiling various files and dependencies. Bear with it. It will prompt you a few times about dependencies. You probably want to enter “yes”. I agreed to everything it asked me, and everything turned out fine. YMMV of course. If everything installs properly, it’ll give you an “OK” at the end.

4) Install your modules. For each module….

$ sudo perl -MCPAN -e 'install Bundle::Name'

$ sudo perl -MCPAN -e 'install Module::Name'

This will install the module and its dependencies. Nice, eh? Again, don’t forget the sudo.

The first time you run this after upgrading CPAN, it may prompt you to configure again (see Step 2). If you accept its offer to try to configure itself automatically, it may just run through everything without a problem.

There are a couple of potential pitfalls with specific modules (such as theLWP::UserAgent / HEAD issue), but most have workarounds, and I haven’t run into anything that wasn’t easily recoverable.

And that’s it!

Did you find this useful? Is there anything I missed?

Statistical for biological research

Neel — Thu, 03 Nov 2016 04:59:48 -0500

There is no disputing the importance of statistical analysis in biological research, but too often it is considered only after an experiment is completed, when it may be too late.

This collection highlights important statistical issues that biologists should be aware of and provides practical advice to help them improve the rigor of their work.

Nature Methods' Points of Significance column on statistics explains many key statistical and experimental design concepts. Other resources include an online plotting tool and links to statistics guides from other publishers.

Address of the bookmark: http://www.nature.com/collections/qghhqm

Bookmarks Biostatistics materials and books

Jit — Tue, 08 Nov 2016 07:42:42 -0600

Biostatistics did not spring fully formed from the brow of R. A. Fisher, but evolved over many years. This process is continuing, although it may not be obvious from the outside. It has been ten years since the first edition of this book appeared (and rather longer since it was begun). Over this time, new areas of biostatistics have been developed and emphases and interpretations have changed

Please bookmarks your favourate biostatistics books in commend sectons ...

Address of the bookmark: http://www.cos.ufrj.br/~bioestatistica/livros/Introduction%20to%20Biostatistics.pdf

CISA: Contig Integrator for Sequence Assembly

Neel — Thu, 15 Dec 2016 05:42:21 -0600

A plethora of algorithmic assemblers have been proposed for the de novo assembly of genomes, however, no individual assembler guarantees the optimal assembly for diverse species. Optimizing various parameters in an assembler is often performed in order to generate the most optimal assembly. However, few efforts have been pursued to take advantage of multiple assemblies to yield an assembly of high accuracy. In this study, we employ various state-of-the-art assemblers to generate different sets of contigs for bacterial genomes. A tool, named CISA, has been developed to integrate the assemblies into a hybrid set of contigs, resulting in assemblies of superior contiguity and accuracy, compared with the assemblies generated by the state-of-the-art assemblers and the hybrid assemblies merged by existing tools. This tool is implemented in Python and requires MUMmer and BLAST+ to be installed on the local machine. The source code of CISA and examples of its use are available at http://sb.nhri.org.tw/CISA/.

Address of the bookmark: http://sb.nhri.org.tw/CISA/en/CISA