Address of the bookmark: https://bioconda.github.io/recipes/snakemake/README.html

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/

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/

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://liulab-dfci.github.io/software/

Personal Genome Variation: SVs
Human Genome Annotation: Processing Next-Gen Sequencing Data
Comparative Genomics: Pseudogenes as Molecular Fossils
Protein Structure and Function: Macromolecular Motions
Analysis of Diverse Networks
Genomics at the Forefront of Data Science

Lab page: http://www.gersteinlab.org/

Applications are invited for admission to the Ph.D. programme in the Department of Biophysics, Molecular Biology & Bioinformatics, University of Calcutta for the year 2014 from eligible candidates who would be placed under the departmental teachers or affiliated research supervisors for the pursuance of their Ph.D. programme.

Candidates are requested to download the Ph.D. admission test application form from the University website and apply in the prescribed proforma by paying Rs. 100/- through a challan available through different University Cash counters. The challan is to be duly forwarded through the Head, Department of Biophysics, Molecular Biology & Bioinformatics, University of Calcutta.

The completed application form with a copy of the paid challan is to be submitted to the office of the Department by April 16, 2014.

Syllabus for the Test: The questions for the admission test and interview will be based on topics in the following areas:

Mathematical methods, Molecular and Cellular Biophysics, Molecular and Cell Biology, Biochemistry, Genetics, Plant Biology, Developmental biology, Neurobiology, Biotechnology and Bioinformatics.

However, the interview will be primarily based on the research emphasis of the candidate. Candidates must clearly indicate the program in which they want to apply.

Date of Admission test : April 22, 2014 (Tuesday)

Date of publication of selection list for the interview : April 22, 2014(Tuesday)

Date of Interview : April 23, 2014 (Wednesday)

Number of vacancies for the Ph.D. programme : 12

Reservation policy will be followed as per rules.

Candidates with valid NET/GATE/M.Phil. or equivalent qualifications are not required to appear at the admission test but would need to qualify in the interview.

Advertisement:

http://www.caluniv.ac.in/admission%20notice/PHD_BIO_PHYSICS.pdf

Welcome to phylobabble.org, a discussion forum for phylogenetic theory and applications. The primary goal of this forum is to discuss best practice and new developments in phylogenetics. Although we do have a Troubleshooting category for getting feedback on analyses, this is not a help site for running phylogenetics programs.

A great place to chat about phylogenetics for researchers and the broader community of students and science-interested citizens. 

Address of the bookmark: http://phylobabble.org/

Algorithms scripts @ https://github.com/jschendel/bioinformatics-algorithms-coursera

Address of the bookmark: https://github.com/jorvis/biocode

1. SPAdes: An assembler specifically designed for single-cell and multi-cell bacterial genomes, as well as small eukaryotic genomes.

2. ABySS: A parallelized assembler for large genomes that uses de Bruijn graphs.

3. Velvet: Another de Bruijn graph-based assembler optimized for short-read sequencing data.

4. SOAPdenovo: A de Bruijn graph-based assembler designed for short reads, widely used for assembling large and complex genomes.

5. MaSuRCA: A hybrid assembler that combines data from multiple sequencing technologies, such as Illumina and PacBio.

6. Canu: A long-read assembler optimized for PacBio and Oxford Nanopore sequencing data.

7. Flye: A long-read assembler suitable for bacterial and small eukaryotic genomes.

8. SMARTdenovo: An assembler designed for long reads, particularly suited for PacBio data.

9. SPAdes Long Read (SPAdesLR): An extension of SPAdes for long-read data, such as those from PacBio or Nanopore.

10. Minia: An assembler optimized for low memory consumption, suitable for small and medium-sized genomes.

11. Unicycler: A hybrid assembler that combines short and long reads for circular bacterial genome assembly.

12. wtdbg2: A de Bruijn graph assembler for long reads, efficient for very large genomes.

13. Shasta: A long-read assembler that uses the Overlap-Layout-Consensus approach, suitable for PacBio and Nanopore data.

14. Sparc: An assembler designed to handle noisy long reads from Nanopore sequencing.

15. CANA: An assembler for metagenomic data, particularly for complex and diverse microbial communities.

16. Ra Assembler: A metagenome assembler for long reads, designed for highly complex metagenomic samples.

Please note that the field of bioinformatics is constantly evolving, and new assembly tools may have emerged since my last update. Additionally, the performance of these tools can vary depending on the characteristics of the sequencing data and the genome being assembled. When selecting an assembly tool, consider the specific requirements of your project, the available data types, and the computational resources at your disposal. Always refer to the respective tool's documentation and publications for the most up-to-date information and recommendations.