This position will have a significant focus on providing analytical support for next generation sequencing data analysis – Exome-sequencing, Targetted sequencing as well as high-throughput genotyping on Illumina platform.

Job location:

Genome Research Chair
King Saud University, Riyadh-11451
KSA

Interested candidate may forward their CV to grcksu@gmail.com

Address of the bookmark: https://github.com/cauyrd/SVfinder

Required Qualifications: Masters in physics/chemistry/mathematics (or) MTech in bioengineering, chemical (or) Masters in any traditional field of science with outstanding performance throughout the program. Candidate should have cleared GATE/UGC-CSIR examinations. Applicant should have done basic mathematics courses like calculus, differential equations, numerical analysis etc in their degree program and have obtained good grades in those courses. Knowledge of MATLAB and C or at least one traditional programming language is absolutely necessary. Strong inclination to understand biological concepts is a must for this research work as this project is about modeling biological systems.

Salary: A fixed salary of Rs 18000 PM including HRA will be paid.

Last date for application: This advertisement is open until suitable candidate is found for the project.

Preferred Qualifications: - Expertise in dynamical systems theory, bifurcation theory, numerical simulations, parameter estimation.

Independence and high motivation for carrying out interdisciplinary research. - Excellent communication skills and ability to work independently. - Good working habits.

Interested candidates should submit both curriculum vitae and statement of interest in PDF format to sriramk@iiitd.ac.in and should clearly mention in the subject "Application for SRF".

Address of the bookmark: https://www.nature.com/articles/srep20802

Our research is at the crossroad between cell biology, ecological genomics, systems biology, molecular evolution and population genetics. We study the architecture and evolution of protein and signalling networks.

More at http://landrylab.ibis.ulaval.ca/

SynVisio requires two files to run:

• The simplified gff file that was used as an input for a McScanX query.
• The collinearity file generated as an output by McScanX for the same input query.
• Optional track file in bedgraph format to annotate the generated charts.

SynVisio offers different types of visualizations such as Linear Parallel plots, Hive plots, Stacked Parallel Plots and Dot plots. Users can configure the type of plots required and then choose the source and the target chromosomes that need to be mapped. Users also have option to download the generated visualizations in publication ready SVG or PNG formats.

Address of the bookmark: https://synvisio.github.io/#/

1.automatic learning of chemical reactivity and metabolism,
2.simulation of NMR spectra,
3.modelling of properties of ionic liquids, and
4.representation of molecular chirality.

More at http://joao.airesdesousa.com/

panacus supports the following calculations:

• coverage histogram
• pangenome growth statistics
• path-/group-resolved coverage table

Address of the bookmark: https://github.com/marschall-lab/panacus

The First time when you login to the remotehost from a localhost, it will display the host key not found message and you can give “yes” to continue. The host key of the remote host will be added under .ssh2/hostkeys directory of your home directory, as shown below.

localhost$ ssh -l jit remotehost.example.com

jit@remotehost.example.com password:

remotehost.example.com$

The Second time when you login to the remote host from the localhost, it will prompt only for the password as the remote host key is already added to the known hosts list of the ssh client.

localhost$ ssh -l jit remotehost.example.com
jit@remotehost.example.com password:
remotehost.example.com$

For some reason, if the host key of the remote host is changed after you logged in for the first time, you may get a warning message as shown below. This could be because of various reasons such as 1) Sysadmin upgraded/reinstalled the SSH server on the remote host 2) someone is doing malicious activity etc., The best possible action to take before saying “yes” to the message below, is to call your sysadmin and identify why you got the host key changed message and verify whether it is the correct host key or not.

localhost$ ssh -l jit remotehost.example.com

jit @remotehost.example.com's password:
remotehost$

4. Debug SSH Client:

Sometimes it is necessary to view debug messages to troubleshoot any SSH connection issues. For this purpose, pass -v (lowercase v) option to the ssh as shown below.

Example without debug message:

        localhost$ ssh -l jit remotehost.example.com
        warning: Connecting to remotehost.example.com failed: No address associated to the name
        localhost$

Example with debug message:

        locaclhost$ ssh -v -l jit remotehost.example.com
        debug: SshConfig/sshconfig.c:2838/ssh2_parse_config_ext: Metaconfig parsing stopped at line 3.
        debug: SshConfig/sshconfig.c:637/ssh_config_set_param_verbose: Setting variable 'VerboseMode' to 'FALSE'.
        debug: SshConfig/sshconfig.c:3130/ssh_config_read_file_ext: Read 17 params from config file.
        debug: Ssh2/ssh2.c:1707/main: User config file not found, using defaults. (Looked for '/home/jit/.ssh2/ssh2_config')
        debug: Connecting to remotehost.example.com, port 22... (SOCKS not used)
        warning: Connecting to remotehost.example.com failed: No address associated to

5. Escape Character: (Toggle SSH session, SSH session statistics etc.)

Escape character ~ get’s SSH clients attention and the character following the ~ determines the escape command.
Toggle SSH Session: When you’ve logged on to the remotehost using ssh from the localhost, you may want to come back to the localhost to perform some activity and go back to remote host again. In this case, you don’t need to disconnect the ssh session to the remote host. Instead follow the steps below.

i. Login to remotehost from localhost: localhost$ssh -l jit remotehost
ii. Now you are connected to the remotehost: remotehost$
iii. To come back to the localhost temporarily, type the escape character ~ and Control-Z. When you type ~ you will not see that immediately on the screen until you press and press enter. So, on the remotehost in a new line enter the following key strokes for the below to work: ~

    remotehost$ ~^Z
    [1]+  Stopped                 ssh -l jit remotehost
    localhost$

iv. Now you are back to the localhost and the ssh remotehost client session runs as a typical unix background job, which you can check as shown below:

    localhost$ jobs
    [1]+  Stopped                 ssh -l jit remotehost

v. You can go back to the remote host ssh without entering the password again by bringing the background ssh remotehost session job to foreground on the localhost

    localhost$ fg %1
    ssh -l jit remotehost
    remotehost$

https://iopscience.iop.org/article/10.1088/2632-2153/ab7e19/pdf

Address of the bookmark: https://github.com/gguptaiitd/NEAT