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User: Vimalkumar Velayudhan

gravatar for Vimalkumar Velayudhan
Reputation:
190
Status:
Trusted
Location:
Ireland
Website:
https://vimal.io/
Scholar ID:
Google Scholar Page
Last seen:
7 months ago
Joined:
8 years, 8 months ago
Email:
c******@vimal.io

Bioinformatics Software Developer & Linux System Administrator

I'm currently developing BioVM - a virtual machine with pre-configured Bioinformatics software.

Previously, I have contributed in the development of software like ITQuery, RiboPlot and riboSeqR wrapper (hosted at RiboGalaxy) and VIGA. Some of this work has been included in scientific publications.

A complete list of the work I have done is available.

Posts by Vimalkumar Velayudhan

<prev • 33 results • page 1 of 4 • next >
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Tutorial: Getting the lineage of an organism from NCBI taxonomy data
... This is a method I followed to get an organism's complete lineage from [NCBI][1] taxonomy data. The procedure involves: 1. Creating a MySQL database. 2. Initialising the database with the [BioSQL][2] schema. 3. Downloading and importing the NCBI taxonomy data into the database. 4. Using a python sc ...
python tutorial taxonomy biosql written 11 months ago by Vimalkumar Velayudhan • 190
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Comment: C: OrthoMCL installation on Ubuntu Linux
... Did you use the same password in the config file i.e., the password used while creating the orthomcl user? If it still doesn't work, please post your complete orthomcl.config file. You can remove the password setting. ...
written 11 months ago by Vimalkumar Velayudhan • 190
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Comment: C: OrthoMCL installation on Ubuntu Linux
... There needs to be a `dbVendor=mysql` setting in addition to the `dbConnectString=...` in the config file. If you had created the configuration file by copying the orthomcl.config.template, this should already be present. ...
written 11 months ago by Vimalkumar Velayudhan • 190
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Answer: A: Trying to install RSeQC-python package
... You haven't mentioned what Linux distribution this is. If you are on a Debian/Ubuntu system, you need to install the system library that python-lzo requires i.e., **liblzo2-dev**. On RPM based systems like Fedora or openSUSE, this package is most likely named **lzo2-devel**. ...
written 11 months ago by Vimalkumar Velayudhan • 190
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Comment: C: Cutadapt installation - user defined directory
... Cutadapt has minimal dependencies so with Python 3, you could also do the following assuming the python3-venv module is installed: # install latest version python3 -m venv cutadapt source cutadapt/bin/activate pip install cutadapt deactivate # install version 1.14 pyt ...
written 11 months ago by Vimalkumar Velayudhan • 190
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Answer: C: Simple visual output of Pairwise Sequence alignment
... I had implemented something similar in RiboPlot to mark the positions of start and stop codons in three reading frames. This was done using [Matplotlib][1]. Code is on [github][2] and the plot is generated in the [plot_profile][3] function. ![enter image description here][4] [1]: https://matplo ...
written 13 months ago by Vimalkumar Velayudhan • 190
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Comment: C: Obisilva (obitools) not working
... With obitools version 1.2.11, the `obisilva --ssu --parc` command works fine. You should try again after updating obitools if you have an older version. ...
written 13 months ago by Vimalkumar Velayudhan • 190
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Comment: C: OrthoMCL installation on Ubuntu Linux
... Your hard disk is full. You could try to free some disk space by removing files you don't need or moving input/output files from previous steps. Another possibility is to move the database directory to a new location with free space i.e., a separate disk partition. Here is a tutorial on how to do th ...
written 13 months ago by Vimalkumar Velayudhan • 190
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Comment: C: docker container for Pindel
... No problem! `/opt/pindel-0.2.5b8/pindel` argument isn't required as it appears pindel is run by default when starting the container. Looks like pindel2vcf is a separate Docker image https://hub.docker.com/r/mgibio/pindel2vcf ...
written 13 months ago by Vimalkumar Velayudhan • 190
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Comment: C: docker container for Pindel
... The image on Docker hub doesn't have the *latest* tag which `docker pull` looks for by default. The only available version is [tagged][1] v0.2.5b8. You should be able to pull it using: docker pull mgibio/pindel:v0.2.5b8 [1]: https://hub.docker.com/r/mgibio/pindel/tags/ ...
written 13 months ago by Vimalkumar Velayudhan • 190

Latest awards to Vimalkumar Velayudhan

Popular Question 11 months ago, created a question with more than 1,000 views. For How to - Install Python packages in a virtual environment (virtualenv)
Popular Question 13 months ago, created a question with more than 1,000 views. For OrthoMCL installation on Ubuntu Linux
Appreciated 15 months ago, created a post with more than 5 votes. For OrthoMCL installation on Ubuntu Linux
Scholar 18 months ago, created an answer that has been accepted. For A: ClustAGE error on Linux - "Support directory 'bin' is not present"
Autobiographer 23 months ago, has more than 80 characters in the information field of the user's profile.
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