Walk in interview for guest faculty in Pondicherry University, India. For more information please visit http://www.bicpu.edu.in/bioinfor140814.pdf

https://github.com/tanghaibao/jcvi

More at https://github.com/tanghaibao/jcvi/wiki

Address of the bookmark: https://github.com/tanghaibao/jcvi

DNAApp: for iPhone/iPad

This is an iOS app that allows for the opening and analysis of DNA sequencing files - ab1. It includes handy tools such as "Reverse Complement", "Jump to", "Copy and Paste sequences", fast and end scrolling, "Chromatogram adjustments", and "Searching for segments" functions.
When used in combination with other zip apps, and also web-tools like Blast, this app allows you to analyze, and also determine the quality of your sequencing files.
This app works with cloud storage access like Dropbox to your sequencing files.
This is now compatible with the new update for iOS 7.1.
Demo video can be found at: https://www.youtube.com/watch?v=mXeo9hXdZgM 

More @ https://itunes.apple.com/us/app/dnaapp/id854944694?mt=8

DNAApp: For android

This is the first android app that allows for the opening and analysis of DNA sequencing files - ab1. It includes handy tools such as "Reverse Complement", "Jump to", fast and end scrolling, "Chromatogram adjustments", amino acid translations, "export to fasta", and "searching for segment" function.

• When used in combination with other zip apps, and also web-tools like Blast, this app allows you to analyze, and also determine the quality of your sequencing files.
• This app works with cloud storage access like Dropbox to your sequencing files.
• This is now compatible with the new update for Android 4.4.2.

More @  https://play.google.com/store/apps/details?id=bii.seqdatreader&hl=en

BioGene:iPhone/iPad

BioGene is an information tool for biological research. Use BioGene to learn about gene function. Enter a gene symbol or gene name, for example "CDK4" or "cyclin dependent kinase 4" and BioGene will retrieve its gene function and references into its function (GeneRIF).

• BioGene was produced in affiliation with the Computational Biology Center at Memorial Sloan-Kettering Cancer Center with primary information from Entrez Gene at the NCBI.

More @  https://itunes.apple.com/us/app/biogene/id333180084?mt=8

Mentha - the interactome browser: Android

About: mentha - the interactome browser, is a project that offers protein-protein physical/enzymatic interaction information from various sources. For more details about mentha, visit mentha's website. This client application is an independent project. This application is designed to allow you to search proteins on the go.

Key features (Also in website):

• Search proteins by UniProt IDs, gene name or keywords
• Collect proteins from different queries.
• Spot common interactors in clusters.
• Easily distinguish between proteins from Homo sapiens and other organisms (Yellow rounded rectangles)
• Click on edges(links) to get scientific evidence.
• Click on proteins to see descriptions.

More @  https://play.google.com/store/apps/details?id=com.sinnefa.mentha&hl=en

GeneIndex: iPhone/iPad

GeneIndex quickly provides information about genes from various sources. It also includes a RSS reader for journal feeds as well as a PubMed viewer.

Key Features:

• Look up genes by symbol or description.
• Gene indexes for many mammals, plants, invertebrates, and bacteria.
• Link to gene info on websites.
• Download files for offline use. (.pdf, .mp3, .m4v, .doc, .ppt, .xls )
• transfer files via open in, email, or iTunes file sharing
• View RSS feeds for journals
• Query GeneRIF interactions, COSMIC mutations, and CNV data for cell lines.
• Does not require a network connection for local databases.
• View and search PubMed in table view.

GeneIndex provides a convenient and portable way to lookup gene symbols while at a seminar, conference, or lab meeting. Genes are linked to common life science websites such as NCBI, COSMIC, KEGG, PubMed, SymAtlas, UCSC genome browser, Pathway Commons, Genatlas, Wikipedia, HUGO, and OMIM. GeneRIF gene interactions can also be queried.

• Keep current on the scientific literature. GeneIndex includes a RSS reader and web browser for browsing popular journals like Nature, Science, and Cell. You can also add your own RSS feeds. PDFs and podcasts can be saved as files that you can view on the device or email as attachments.
• Examine the status of genes in common cell lines. A subset of COSMIC containing cell lines can be queried for mutations. Copy Number Variation (CNV) plots from cell lines profiled by GSK and Sanger are also linked to genes.

More @  https://itunes.apple.com/us/app/geneindex/id319769866?mt=8

Genome Voyager: iPad

Gain first hand experience identifying the genomic basis of disease by analyzing cases with whole genome sequencing data that have been published for research and learning purposes.

• Visualize whole human genome sequencing data including small variations, copy number variations (CNVs), and loss of heterozygosity (LOH) events
• Quickly find variants of interest by filtering variants based on associated genes, functional impact, allele frequency in data sets, and cross-references with various genomic databases.
• Collaborate on variant assessments with other researchers and academics to improve knowledge of both pathogenic and benign variants.
  To use Genome Voyager, users must join Genome Voyager’s community of researchers and academics. Visit http://voyager.completegenomics.com to signup.

More @  https://itunes.apple.com/us/app/genome-voyager/id637353801?mt=8

YeastGenome: iPhone/iPad

Use YeastGenome to quickly find fundamental information about Saccharomyces cerevisae genes and chromosomal features. Search gene names, gene descriptions or browse the database to find information about your favorite gene, as well as more detailed information such as Gene Ontology, mutant phenotype, and protein and genetic interaction data.
YeastGenome contains the latest from the Saccharomyces Genome Database (www.yeastgenome.org) in an on bound app database. As more detailed information is presented the app switches to web services access to SGD, and then for even more details provides complete information via hyperlinks to the appropriate SGD database pages.

Key features:

• Search using gene name or keywords
• Browse by feature type
• Save your favorite features
• Can be used in airplane mode
• Email information about features to collaborators

What's New in Version 1.8.1

• This update is required to provide continued functionality. Some of the data provided by this app accesses the SGD service using a method that is changing in May 2013. This version provides changes to allow access to continue. The on board database of yeast gene information has also been updated to March 2013.

More @  https://itunes.apple.com/us/app/yeastgenome/id520868597?mt=8

SNPdbe: iPhone/iPad

SNPdbe — SNP database of effects, with predictions of computationally annotated functional impacts of SNPs. Database entries represent nsSNPs in dbSNP and 1000 Genomes collection, as well as variants from UniProt and PMD. SAASs come from >2600 organisms; ‘human’ being the most prevalent. The impact of each SAAS on protein function is predicted using the SNAP and SIFT algorithms and augmented with experimentally derived function/structure information and disease associations from PMD, OMIM and UniProt.

More @  https://itunes.apple.com/us/app/snpdbe/id588289719?mt=8

SimGene: iPhone/iPad / Android

SimGene: for iPhone/iPad

SimGene is an iPhone/iPad/iPod touch application designed for molecular biologists, bioinformaticians and medical researchers. The application interfaces with Simbiot, Ensembl, NCBI, Gene Ontology, KEGG Pathways, PubMed, Genomic Variations and many other databases to retrieve up-to-date annotation information for over 30 species, based on gene symbol search. The application provides gene and transcript cross reference information for NCBI, Ensembl, RefSeq and UniProt. SimGene also contains an integrated genome browser with information on genes, transcripts, exons and SNPs.

More @  https://itunes.apple.com/us/app/simgene/id427772349?mt=8

SimGene: for Android

bioinformaticians and medical researchers. The application interfaces with Simbiot,Ensembl, NCBI, Gene Ontology, KEGG Pathways, PubMed, Genomic Variations andmany other databases to retrieve up-to-date annotation information for over 30species, based on gene symbol search. The application provides gene and transcriptcross reference information for NCBI, Ensembl, RefSeq and UniProt. SimGene alsocontains an integrated genome browser with information on genes, transcripts,exons and SNPs.

More @  https://play.google.com/store/apps/details?

TimeTree: iPhone/iPad

TimeTree is a public knowledge-base for information on the evolutionary timescale of life. This application allows easy exploration of the thousands of divergence times among organisms in the scientific literature. A tree-based (hierarchical) system is used to identify all published molecular time estimates bearing on the divergence of two chosen organisms, such as species, compute summary statistics, and present the results. Names of two taxa to be compared are entered in the search window and the results are presented on a set of self-explanatory tabs.

• TimeTree 3.0 was released September 27, 2011 with new data from 1209 studies including 25342 time nodes. We will be adding more data in the future as it comes in from researchers.
• TimeTree is jointly directed by Blair Hedges (Pennsylvania State University) and Sudhir Kumar (Arizona State University). This project has been supported, in part, by grants from the National Science Foundation, National Institutes of Health, NASA Astrobiology Institute, and Science Foundation of Arizona.

More @  https://itunes.apple.com/us/app/timetree/id372842500?mt=8

GeneGroove: iPhone/iPad

GeneGroove is the first application to create a music melody from DTC-Genomics data. If you own 23andMe (Mountain View, CA) personal genomic results, GeneGroove will create for you a unique melody intimately based on your 23andMe genome informations. The music in you.

• After uploading your 23andMe raw data onto your iPhone via iTunes, GeneGroove will analyze your genome informations and generate a unique identifier key. This key, called the GeNumber, will embed the uniqueness of your genome data while keeping your privacy safe, and will be used by GeneGroove to generate your music melody.
• The GeNumber doesn't contain anymore genomic information but it is based on your genome and it is unique, it is yours. It will be used in upcoming Portable Genomics applications to mix and remix music, manipulate sounds and share your art with your friends and family.

More @  https://itunes.apple.com/us/app/genegroove/id492247404?mt=8

Address of the bookmark: https://github.com/thackl/gggenomes

Our present objectives is to identify and isolate the substances secreted by Spalax cells, resolve with which components they interact that are active only on cancer cells, in order to unravel the biological mechanisms and pathways that evolved in Spalax cell machinery and ultimately lead to the death of cancer-cells. The study could attest to be a breakthrough in cancer research, using the long lived, hypoxia- and cancer-tolerant Spalax as a significant biological resource for biomedical research that hopefully could open new horizons in treatment and prevention of cancer in humans.

Contact: The applications should be submitted, together with extended CV and bibliography, summary of past accomplishments, and contact information of 3 referees, to Prof of Research Aaron Avivi (aaron@research.haifa.ac.il) AND Dr. Imad Shams (imadshams@gmail.com). (http://bit.ly/1lywShk) aaron@research.haifa.ac.il

More at http://evolution.haifa.ac.il/index.php/29-people/personal-websites/77-personal-site-avivi

Your tasks will consist of:

Advanced bioinformatics analyses within research projects across Sweden, including key involvement in a major research effort in conifer genomics.
Development of bioinformatics tools and workflows.
Educating other scientists in bioinformatics through collaboration within supported projects, teaching at national courses, and through participating in various networks.
Taking part in the continuous development of NBIS/SciLifeLab at a national level

More at https://www.uu.se/en/about-uu/join-us/details/?positionId=518909

conda is a tool for managing and deploying applications, environments and packages.

options:
-h, --help Show this help message and exit.
-v, --verbose Can be used multiple times. Once for detailed output, twice for INFO logging, thrice for DEBUG logging, four times for TRACE logging.
--no-plugins Disable all plugins that are not built into conda.
-V, --version Show the conda version number and exit.

commands:
The following built-in and plugins subcommands are available.

COMMAND
activate Activate a conda environment.
clean Remove unused packages and caches.
commands List all available conda subcommands (including those from plugins). Generally only used by tab-completion.
compare Compare packages between conda environments.
config Modify configuration values in .condarc.
create Create a new conda environment from a list of specified packages.
deactivate Deactivate the current active conda environment.
doctor Display a health report for your environment.
env Create and manage conda environments.
export Export a given environment
info Display information about current conda install.
init Initialize conda for shell interaction.
install Install a list of packages into a specified conda environment.
list List installed packages in a conda environment.
notices Retrieve latest channel notifications.
package Create low-level conda packages. (EXPERIMENTAL)
remove (uninstall) Remove a list of packages from a specified conda environment.
rename Rename an existing environment.
repoquery Advanced search for repodata.
run Run an executable in a conda environment.
search Search for packages and display associated information using the MatchSpec format.
update (upgrade) Update conda packages to the latest compatible version.
(base) hp@hp-HP-Z2-Tower-G9-Workstation-Desktop-PC:~/jitendraTEST$ conda create -n jitENV
Retrieving notices: done
Channels:
- ursky
- bioconda
- conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done

==> WARNING: A newer version of conda exists. <==
current version: 25.7.0
latest version: 26.5.0

Please update conda by running

$ conda update -n base -c conda-forge conda

## Package Plan ##

environment location: /home/hp/miniforge3/envs/jitENV

Proceed ([y]/n)? y

Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
# $ conda activate jitENV
#
# To deactivate an active environment, use
#
# $ conda deactivate

(base) hp@hp-HP-Z2-Tower-G9-Workstation-Desktop-PC:~/jitendraTEST$ conda activate jitENV
(jitENV) hp@hp-HP-Z2-Tower-G9-Workstation-Desktop-PC:~/jitendraTEST$ conda install conda-forge::mamba
Channels:
- ursky
- bioconda
- conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done

==> WARNING: A newer version of conda exists. <==
current version: 25.7.0
latest version: 26.5.0

Please update conda by running

$ conda update -n base -c conda-forge conda

## Package Plan ##

environment location: /home/hp/miniforge3/envs/jitENV

added / updated specs:
- conda-forge::mamba

The following packages will be downloaded:

package | build
---------------------------|-----------------
ca-certificates-2026.5.20 | hbd8a1cb_0 127 KB conda-forge
cpp-expected-1.3.1 | h171cf75_0 24 KB conda-forge
fmt-12.1.0 | hff5e90c_0 193 KB conda-forge
libarchive-3.8.7 | gpl_hc2c16d8_101 869 KB conda-forge
libcurl-8.20.0 | hcf29cc6_0 458 KB conda-forge
libgcc-15.2.0 | he0feb66_19 1017 KB conda-forge
libgcc-ng-15.2.0 | h69a702a_19 27 KB conda-forge
libgomp-15.2.0 | he0feb66_19 590 KB conda-forge
libmamba-2.6.2 | hd28c85e_0 2.7 MB conda-forge
libmsgpack-c-6.1.0 | h54a6638_6 39 KB conda-forge
libsolv-0.7.38 | h9463b59_0 509 KB conda-forge
libstdcxx-15.2.0 | h934c35e_19 5.6 MB conda-forge
libxml2-2.15.3 | h49c6c72_0 46 KB conda-forge
libxml2-16-2.15.3 | hca6bf5a_0 547 KB conda-forge
mamba-2.6.2 | hce6dcdd_0 553 KB conda-forge
ncurses-6.6 | hdb14827_0 897 KB conda-forge
nlohmann_json-abi-3.12.0 | h0f90c79_1 4 KB conda-forge
reproc-14.2.7.post0 | hb03c661_1 35 KB conda-forge
reproc-cpp-14.2.7.post0 | hecca717_1 26 KB conda-forge
simdjson-4.6.4 | hb700be7_0 310 KB conda-forge
spdlog-1.17.0 | hab81395_1 192 KB conda-forge
------------------------------------------------------------
Total: 14.6 MB

The following NEW packages will be INSTALLED:

_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-20_gnu
bzip2 conda-forge/linux-64::bzip2-1.0.8-hda65f42_9
c-ares conda-forge/linux-64::c-ares-1.34.6-hb03c661_0
ca-certificates conda-forge/noarch::ca-certificates-2026.5.20-hbd8a1cb_0
cpp-expected conda-forge/linux-64::cpp-expected-1.3.1-h171cf75_0
fmt conda-forge/linux-64::fmt-12.1.0-hff5e90c_0
icu conda-forge/linux-64::icu-78.3-h33c6efd_0
keyutils conda-forge/linux-64::keyutils-1.6.3-hb9d3cd8_0
krb5 conda-forge/linux-64::krb5-1.22.2-ha1258a1_0
libarchive conda-forge/linux-64::libarchive-3.8.7-gpl_hc2c16d8_101
libcurl conda-forge/linux-64::libcurl-8.20.0-hcf29cc6_0
libedit conda-forge/linux-64::libedit-3.1.20250104-pl5321h7949ede_0
libev conda-forge/linux-64::libev-4.33-hd590300_2
libgcc conda-forge/linux-64::libgcc-15.2.0-he0feb66_19
libgcc-ng conda-forge/linux-64::libgcc-ng-15.2.0-h69a702a_19
libgomp conda-forge/linux-64::libgomp-15.2.0-he0feb66_19
libiconv conda-forge/linux-64::libiconv-1.18-h3b78370_2
liblzma conda-forge/linux-64::liblzma-5.8.3-hb03c661_0
libmamba conda-forge/linux-64::libmamba-2.6.2-hd28c85e_0
libmsgpack-c conda-forge/linux-64::libmsgpack-c-6.1.0-h54a6638_6
libnghttp2 conda-forge/linux-64::libnghttp2-1.68.1-h877daf1_0
libsolv conda-forge/linux-64::libsolv-0.7.38-h9463b59_0
libssh2 conda-forge/linux-64::libssh2-1.11.1-hcf80075_0
libstdcxx conda-forge/linux-64::libstdcxx-15.2.0-h934c35e_19
libxml2 conda-forge/linux-64::libxml2-2.15.3-h49c6c72_0
libxml2-16 conda-forge/linux-64::libxml2-16-2.15.3-hca6bf5a_0
libzlib conda-forge/linux-64::libzlib-1.3.2-h25fd6f3_2
lz4-c conda-forge/linux-64::lz4-c-1.10.0-h5888daf_1
lzo conda-forge/linux-64::lzo-2.10-h280c20c_1002
mamba conda-forge/linux-64::mamba-2.6.2-hce6dcdd_0
ncurses conda-forge/linux-64::ncurses-6.6-hdb14827_0
nlohmann_json-abi conda-forge/noarch::nlohmann_json-abi-3.12.0-h0f90c79_1
openssl conda-forge/linux-64::openssl-3.6.2-h35e630c_0
reproc conda-forge/linux-64::reproc-14.2.7.post0-hb03c661_1
reproc-cpp conda-forge/linux-64::reproc-cpp-14.2.7.post0-hecca717_1
simdjson conda-forge/linux-64::simdjson-4.6.4-hb700be7_0
spdlog conda-forge/linux-64::spdlog-1.17.0-hab81395_1
yaml-cpp conda-forge/linux-64::yaml-cpp-0.8.0-h3f2d84a_0
zstd conda-forge/linux-64::zstd-1.5.7-hb78ec9c_6

Proceed ([y]/n)? y

Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(jitENV) hp@hp-HP-Z2-Tower-G9-Workstation-Desktop-PC:~/jitendraTEST$ mamba install -c jitendralab -c bioconda -c conda-forge crossroad -y
jitendralab/noarch ??.?MB @ ??.?MB/s 0.3s
jitendralab/linux-64 ??.?MB @ ??.?MB/s 0.4s
bioconda/linux-64 5.6MB @ 2.9MB/s 1.9s
bioconda/noarch 5.6MB @ 2.5MB/s 2.2s
conda-forge/noarch 26.4MB @ 6.0MB/s 4.5s
conda-forge/linux-64 53.8MB @ 6.7MB/s 8.2s

Transaction

Prefix: /home/hp/miniforge3/envs/jitENV

Updating specs:

- crossroad

Package Version Build Channel Size
─────────────────────────────────────────────────────────────────────────────────────────────────
Install:
─────────────────────────────────────────────────────────────────────────────────────────────────

+ annotated-doc 0.0.4 pyhcf101f3_0 conda-forge Cached
+ annotated-types 0.7.0 pyhd8ed1ab_1 conda-forge Cached
+ anyio 4.13.0 pyhcf101f3_0 conda-forge 147kB
+ argcomplete 3.6.3 pyhd8ed1ab_0 conda-forge Cached
+ aws-c-auth 0.10.3 h3aafcba_1 conda-forge 134kB
+ aws-c-cal 0.9.14 h8e43964_1 conda-forge 57kB
+ aws-c-common 0.13.1 hb03c661_0 conda-forge 242kB
+ aws-c-compression 0.3.2 h16e98cb_1 conda-forge 22kB
+ aws-c-event-stream 0.7.1 h9be7a74_1 conda-forge 59kB
+ aws-c-http 0.11.0 hcbcd92d_1 conda-forge 230kB
+ aws-c-io 0.26.3 h955231c_3 conda-forge 182kB
+ aws-c-mqtt 0.15.2 h8af55cf_3 conda-forge 222kB
+ aws-c-s3 0.12.3 h00bea6e_2 conda-forge 153kB
+ aws-c-sdkutils 0.2.4 h16e98cb_5 conda-forge 59kB
+ aws-checksums 0.2.10 h16e98cb_1 conda-forge 102kB
+ aws-crt-cpp 0.38.3 h7b0d4b4_2 conda-forge 413kB
+ aws-sdk-cpp 1.11.747 h5a171d8_5 conda-forge 4MB
+ azure-core-cpp 1.16.2 h206d751_0 conda-forge 349kB
+ azure-identity-cpp 1.13.3 hed0cdb0_1 conda-forge 251kB
+ azure-storage-blobs-cpp 12.17.0 hf824e48_1 conda-forge 587kB
+ azure-storage-common-cpp 12.13.0 ha7a2c86_0 conda-forge 159kB
+ azure-storage-files-datalake-cpp 12.15.0 h1e5b466_0 conda-forge 304kB
+ backports.zstd 1.5.0 py314h680f03e_0 conda-forge 8kB
+ bedtools 2.31.1 h13024bc_3 bioconda Cached
+ biopython 1.87 py314h5bd0f2a_0 conda-forge 3MB
+ brotli 1.2.0 hed03a55_1 conda-forge Cached
+ brotli-bin 1.2.0 hb03c661_1 conda-forge Cached
+ brotli-python 1.2.0 py314h3de4e8d_1 conda-forge 367kB
+ certifi 2026.5.20 pyhd8ed1ab_0 conda-forge 134kB
+ charset-normalizer 3.4.7 pyhd8ed1ab_0 conda-forge Cached
+ click 8.4.1 pyhc90fa1f_0 conda-forge 105kB
+ colorama 0.4.6 pyhd8ed1ab_1 conda-forge Cached
+ contourpy 1.3.3 py314h97ea11e_4 conda-forge 324kB
+ crossroad 0.3.6 pyh7e60211_0 jitendralab 2MB
+ cycler 0.12.1 pyhcf101f3_2 conda-forge Cached
+ dnspython 2.8.0 pyhcf101f3_0 conda-forge Cached
+ email-validator 2.3.0 pyhd8ed1ab_0 conda-forge 47kB
+ email_validator 2.3.0 hd8ed1ab_0 conda-forge 7kB
+ exceptiongroup 1.3.1 pyhd8ed1ab_0 conda-forge Cached
+ expat 2.8.1 hecca717_0 conda-forge 148kB
+ fastapi 0.136.3 h5ddb490_0 conda-forge 5kB
+ fastapi-cli 0.0.23 pyhcf101f3_0 conda-forge 19kB
+ fastapi-core 0.136.3 pyhcf101f3_0 conda-forge 96kB
+ fastar 0.11.0 py314h0b738fb_0 conda-forge 423kB
+ font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge Cached
+ font-ttf-inconsolata 3.000 h77eed37_0 conda-forge Cached
+ font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge Cached
+ font-ttf-ubuntu 0.83 h77eed37_3 conda-forge Cached
+ fontconfig 2.18.0 h27c8c51_0 conda-forge 281kB
+ fonts-conda-forge 1 hc364b38_1 conda-forge Cached
+ fonttools 4.63.0 pyh7db6752_0 conda-forge 846kB
+ freetype 2.14.3 ha770c72_0 conda-forge Cached
+ gflags 2.2.2 h5888daf_1005 conda-forge 120kB
+ glog 0.7.1 hbabe93e_0 conda-forge 143kB
+ h11 0.16.0 pyhcf101f3_1 conda-forge 39kB
+ h2 4.3.0 pyhcf101f3_0 conda-forge Cached
+ hpack 4.1.0 pyhd8ed1ab_0 conda-forge Cached
+ httpcore 1.0.9 pyh29332c3_0 conda-forge Cached
+ httptools 0.7.1 py314h5bd0f2a_1 conda-forge 99kB
+ httpx 0.28.1 pyhd8ed1ab_0 conda-forge Cached
+ hyperframe 6.1.0 pyhd8ed1ab_0 conda-forge Cached
+ idna 3.17 pyhcf101f3_0 conda-forge 57kB
+ jinja2 3.1.6 pyhcf101f3_1 conda-forge Cached
+ kaleido-core 0.2.1 h3644ca4_0 conda-forge Cached
+ kiwisolver 1.5.0 py314h97ea11e_0 conda-forge 77kB
+ lcms2 2.19.1 h0c24ade_0 conda-forge 251kB
+ ld_impl_linux-64 2.45.1 default_hbd61a6d_102 conda-forge Cached
+ lerc 4.1.0 hdb68285_0 conda-forge Cached
+ libabseil 20260107.1 cxx17_h7b12aa8_0 conda-forge 1MB
+ libarrow 24.0.0 h6f10b76_3_cpu conda-forge 7MB
+ libarrow-acero 24.0.0 h635bf11_3_cpu conda-forge 592kB
+ libarrow-compute 24.0.0 h53684a4_3_cpu conda-forge 3MB
+ libarrow-dataset 24.0.0 h635bf11_3_cpu conda-forge 592kB
+ libarrow-substrait 24.0.0 hb4dd7c2_3_cpu conda-forge 502kB
+ libblas 3.11.0 8_h4a7cf45_openblas conda-forge 19kB
+ libbrotlicommon 1.2.0 hb03c661_1 conda-forge Cached
+ libbrotlidec 1.2.0 hb03c661_1 conda-forge Cached
+ libbrotlienc 1.2.0 hb03c661_1 conda-forge Cached
+ libcblas 3.11.0 8_h0358290_openblas conda-forge 19kB
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+ zlib-ng 2.3.3 hceb46e0_1 conda-forge Cached

Summary:

Install: 186 packages

Total download: 142MB

─────────────────────────────────────────────────────────────────────────────────────────────────

Transaction starting
libgrpc 7.0MB @ 2.3MB/s 3.0s
numpy 8.9MB @ 2.3MB/s 3.8s
matplotlib-base 8.5MB @ 2.0MB/s 4.2s
libarrow 6.5MB @ 2.3MB/s 2.8s
pandas 15.3MB @ 2.5MB/s 6.2s
libopenblas 5.9MB @ 2.3MB/s 2.5s
pyarrow-core 4.8MB @ 1.6MB/s 3.0s
libprotobuf 3.7MB @ 2.4MB/s 1.6s
aws-sdk-cpp 3.6MB @ 3.1MB/s 1.2s
biopython 3.4MB @ 2.0MB/s 1.7s
libgfortran5 2.5MB @ 2.6MB/s 1.0s
libgoogle-cloud 2.6MB @ 2.4MB/s 1.1s
pydantic-core 1.9MB @ 2.7MB/s 0.7s
libarrow-compute 3.0MB @ 1.9MB/s 1.6s
orc 1.5MB @ 2.8MB/s 0.5s
libparquet 1.4MB @ 3.1MB/s 0.5s
pip 1.2MB @ 2.9MB/s 0.4s
libabseil 1.4MB @ 2.2MB/s 0.6s
pillow 1.1MB @ 2.7MB/s 0.4s
libsqlite 955.0kB @ 2.9MB/s 0.3s
libgoogle-cloud-storage 779.6kB @ 2.7MB/s 0.3s
fonttools 846.0kB @ 2.1MB/s 0.4s
libopentelemetry-cpp 934.3kB @ 1.8MB/s 0.5s
libarrow-acero 592.3kB @ 2.2MB/s 0.2s
uvloop 593.4kB @ 1.3MB/s 0.4s
libarrow-dataset 592.2kB @ 2.7MB/s 0.2s
libarrow-substrait 501.9kB @ 1.8MB/s 0.2s
azure-storage-blobs-cpp 587.1kB @ 1.6MB/s 0.3s
libthrift 423.9kB @ 2.8MB/s 0.2s
crossroad 1.8MB @ 663.3kB/s 2.6s
libuv 419.9kB @ 2.3MB/s 0.2s
fastar 423.4kB @ 966.7kB/s 0.3s
aws-crt-cpp 412.5kB @ 2.9MB/s 0.1s
watchfiles 415.6kB @ 1.6MB/s 0.3s
unicodedata2 409.6kB @ 1.8MB/s 0.2s
libopentelemetry-cpp-headers 396.4kB @ 2.2MB/s 0.2s
s2n 388.1kB @ 2.5MB/s 0.1s
brotli-python 367.4kB @ 1.7MB/s 0.1s
websockets 383.0kB @ 1.3MB/s 0.3s
azure-core-cpp 348.7kB @ 2.7MB/s 0.1s
pydantic 346.5kB @ 1.9MB/s 0.2s
contourpy 324.0kB @ 2.3MB/s 0.1s
libpng 317.7kB @ 1.8MB/s 0.2s
azure-storage-files-datalake-cpp 303.8kB @ 1.9MB/s 0.1s
narwhals 284.3kB @ 1.8MB/s 0.2s
fontconfig 280.9kB @ 866.6kB/s 0.2s
python 36.7MB @ 3.0MB/s 12.0s
azure-identity-cpp 250.5kB @ 1.5MB/s 0.1s
lcms2 251.1kB @ 2.0MB/s 0.1s
aws-c-common 242.3kB @ 2.8MB/s 0.1s
libre2-11 213.1kB @ 66.4kB/s 0.1s
aws-c-http 230.3kB @ 1.7MB/s 0.1s
aws-c-mqtt 221.7kB @ 307.2kB/s 0.1s
sqlite 205.4kB @ ??.?MB/s 0.1s
perf_ssr 720.0kB @ 247.3kB/s 2.3s
prometheus-cpp 199.5kB @ 962.8kB/s 0.1s
pyyaml 202.4kB @ 1.6MB/s 0.1s
typer 184.4kB @ 1.9MB/s 0.1s
aws-c-io 181.6kB @ 1.9MB/s 0.1s
aws-c-s3 153.0kB @ 2.2MB/s 0.1s
azure-storage-common-cpp 159.1kB @ 1.8MB/s 0.1s
expat 148.2kB @ ??.?MB/s 0.0s
anyio 146.8kB @ 2.2MB/s 0.1s
glog 143.5kB @ 2.6MB/s 0.1s
seqtk 141.8kB @ 1.8MB/s 0.1s
nlohmann_json 136.2kB @ 2.1MB/s 0.1s
aws-c-auth 134.4kB @ 1.5MB/s 0.1s
certifi 134.2kB @ 1.8MB/s 0.1s
click 105.0kB @ 1.5MB/s 0.1s
gflags 119.7kB @ 148.2kB/s 0.1s
urllib3 103.6kB @ ??.?MB/s 0.0s
aws-checksums 101.6kB @ ??.?MB/s 0.0s
fastapi-core 95.5kB @ ??.?MB/s 0.0s
libmpdec 92.4kB @ ??.?MB/s 0.0s
packaging 91.6kB @ ??.?MB/s 0.0s
libutf8proc 86.0kB @ ??.?MB/s 0.0s
kiwisolver 77.4kB @ ??.?MB/s 0.0s
libexpat 77.3kB @ 885.4kB/s 0.1s
pydantic-extra-types 73.9kB @ ??.?MB/s 0.0s
markdown-it-py 69.0kB @ ??.?MB/s 0.0s
requests 68.7kB @ ??.?MB/s 0.0s
rich-click 64.4kB @ ??.?MB/s 0.0s
aws-c-event-stream 59.3kB @ ??.?MB/s 0.0s
starlette 63.7kB @ ??.?MB/s 0.0s
aws-c-sdkutils 59.1kB @ ??.?MB/s 0.0s
aws-c-cal 56.9kB @ ??.?MB/s 0.0s
idna 56.9kB @ ??.?MB/s 0.0s
uvicorn 56.3kB @ ??.?MB/s 0.0s
pydantic-settings 52.3kB @ ??.?MB/s 0.0s
email-validator 46.8kB @ ??.?MB/s 0.0s
libuuid 40.2kB @ ??.?MB/s 0.0s
h11 39.1kB @ ??.?MB/s 0.0s
python-multipart 37.8kB @ ??.?MB/s 0.0s
rich-toolkit 32.9kB @ ??.?MB/s 0.0s
upsetplot 28.0kB @ ??.?MB/s 0.0s
libstdcxx-ng 27.8kB @ ??.?MB/s 0.0s
libgfortran 27.7kB @ ??.?MB/s 0.0s
re2 27.5kB @ ??.?MB/s 0.0s
markupsafe 27.4kB @ ??.?MB/s 0.0s
pyarrow 26.8kB @ ??.?MB/s 0.0s
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libblas 18.8kB @ ??.?MB/s 0.0s
httptools 99.0kB @ ??.?MB/s 0.4s
liblapack 18.8kB @ ??.?MB/s 0.0s
libcblas 18.8kB @ ??.?MB/s 0.0s
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backports.zstd 7.5kB @ ??.?MB/s 0.0s
python_abi 7.0kB @ ??.?MB/s 0.0s
fastapi 4.8kB @ ??.?MB/s 0.0s
uvicorn-standard 4.1kB @ ??.?MB/s 0.0s
rich-argparse 26.8kB @ ??.?MB/s 0.2s
plotly-upset-hd 356.0kB @ 181.5kB/s 1.8s
Linking seqkit-2.13.0-he881be0_0
Linking bedtools-2.31.1-h13024bc_3
Linking seqtk-1.5-h577a1d6_1
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Linking zlib-ng-2.3.3-hceb46e0_1
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Linking xorg-libxdmcp-1.1.5-hb03c661_1
Linking libgfortran5-15.2.0-h68bc16d_19
Linking libpng-1.6.58-h421ea60_0
Linking libbrotlicommon-1.2.0-hb03c661_1
Linking libjpeg-turbo-3.1.4.1-hb03c661_0
Linking libdeflate-1.25-h17f619e_0
Linking lerc-4.1.0-hdb68285_0
Linking libsqlite-3.53.1-h0c1763c_0
Linking libffi-3.5.2-h3435931_0
Linking tk-8.6.13-noxft_h366c992_103
Linking azure-core-cpp-1.16.2-h206d751_0
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Linking libutf8proc-2.11.3-hfe17d71_0
Linking libopentelemetry-cpp-headers-1.26.0-ha770c72_0
Linking zlib-1.3.2-h25fd6f3_2
Linking snappy-1.2.2-h03e3b7b_1
Linking nlohmann_json-3.12.0-h54a6638_1
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Linking libevent-2.1.12-hf998b51_1
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Linking qhull-2020.2-h434a139_5
Linking libxcb-1.17.0-h8a09558_0
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Linking libbrotlidec-1.2.0-hb03c661_1
Linking libtiff-4.7.1-h9d88235_1
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Linking nss-3.118-h445c969_0
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Linking azure-storage-common-cpp-12.13.0-ha7a2c86_0
Linking libprotobuf-6.33.5-h6eeba95_1
Linking libre2-11-2025.11.05-h0dc7533_1
Linking prometheus-cpp-1.3.0-ha5d0236_0
Linking aws-c-compression-0.3.2-h16e98cb_1
Linking aws-checksums-0.2.10-h16e98cb_1
Linking aws-c-sdkutils-0.2.4-h16e98cb_5
Linking aws-c-cal-0.9.14-h8e43964_1
Linking glog-0.7.1-hbabe93e_0
Linking libthrift-0.22.0-h7d032f7_2
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Linking lcms2-2.19.1-h0c24ade_0
Linking openjpeg-2.5.4-h55fea9a_0
Linking azure-storage-blobs-cpp-12.17.0-hf824e48_1
Linking re2-2025.11.05-h5301d42_1
Linking aws-c-io-0.26.3-h955231c_3
Linking libblas-3.11.0-8_h4a7cf45_openblas
Linking fontconfig-2.18.0-h27c8c51_0
Linking freetype-2.14.3-ha770c72_0
Linking brotli-1.2.0-hed03a55_1
Linking azure-storage-files-datalake-cpp-12.15.0-h1e5b466_0
Linking libgrpc-1.78.1-h1d1128b_0
Linking aws-c-event-stream-0.7.1-h9be7a74_1
Linking aws-c-http-0.11.0-hcbcd92d_1
Linking libcblas-3.11.0-8_h0358290_openblas
Linking liblapack-3.11.0-8_h47877c9_openblas
Linking libopentelemetry-cpp-1.26.0-h9692893_0
Linking aws-c-auth-0.10.3-h3aafcba_1
Linking aws-c-mqtt-0.15.2-h8af55cf_3
Linking libgoogle-cloud-3.5.0-h25dbb67_0
Linking aws-c-s3-0.12.3-h00bea6e_2
Linking libgoogle-cloud-storage-3.5.0-hdbdcf42_0
Linking aws-crt-cpp-0.38.3-h7b0d4b4_2
Linking aws-sdk-cpp-1.11.747-h5a171d8_5
Linking python_abi-3.14-8_cp314
Linking font-ttf-dejavu-sans-mono-2.37-hab24e00_0
Linking tzdata-2025c-hc9c84f9_1
Linking font-ttf-ubuntu-0.83-h77eed37_3
Linking font-ttf-inconsolata-3.000-h77eed37_0
Linking font-ttf-source-code-pro-2.038-h77eed37_0
Linking fonts-conda-forge-1-hc364b38_1
Linking orc-2.3.0-h21090e2_0
Linking python-3.14.5-habeac84_100_cp314
Linking kaleido-core-0.2.1-h3644ca4_0
Linking libarrow-24.0.0-h6f10b76_3_cpu
Linking libparquet-24.0.0-h7376487_3_cpu
Linking libarrow-compute-24.0.0-h53684a4_3_cpu
Linking libarrow-acero-24.0.0-h635bf11_3_cpu
Linking libarrow-dataset-24.0.0-h635bf11_3_cpu
Linking libarrow-substrait-24.0.0-hb4dd7c2_3_cpu
Linking pip-26.1.1-pyh145f28c_0
Linking tomli-2.4.1-pyhcf101f3_0
Linking six-1.17.0-pyhe01879c_1
Linking pysocks-1.7.1-pyha55dd90_7
Linking hyperframe-6.1.0-pyhd8ed1ab_0
Linking hpack-4.1.0-pyhd8ed1ab_0
Linking backports.zstd-1.5.0-py314h680f03e_0
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Linking sniffio-1.3.1-pyhd8ed1ab_2
Linking mdurl-0.1.2-pyhd8ed1ab_1
Linking narwhals-2.21.2-pyhcf101f3_0
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Linking colorama-0.4.6-pyhd8ed1ab_1
Linking typing_extensions-4.15.0-pyhcf101f3_0
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Linking tqdm-4.67.3-pyh8f84b5b_0
Linking python-kaleido-0.2.1-pyhd8ed1ab_0
Linking python-multipart-0.0.29-pyhcf101f3_0
Linking python-dotenv-1.2.2-pyhcf101f3_0
Linking argcomplete-3.6.3-pyhd8ed1ab_0
Linking python-dateutil-2.9.0.post0-pyhe01879c_2
Linking h2-4.3.0-pyhcf101f3_0
Linking dnspython-2.8.0-pyhcf101f3_0
Linking markdown-it-py-4.2.0-pyhd8ed1ab_0
Linking plotly-6.6.0-pyhd8ed1ab_0
Linking exceptiongroup-1.3.1-pyhd8ed1ab_0
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(jitENV) hp@hp-HP-Z2-Tower-G9-Workstation-Desktop-PC:~/jitendraTEST$ crossroad -h

Usage: crossroad [OPTIONS]

Run the main croSSRoad analysis pipeline, or manage jobs.

╭─ Options ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --version -v Show version, logo, citation, and links. │
│ --install-completion Install completion for the current shell. │
│ --show-completion Show completion for the current shell, to copy it or customize the installation. │
│ --help -h Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Mode Selection ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --api -a Run the Crossroad web API server. │
│ --slurm -s Submit the analysis job to a Slurm cluster. │
│ --job-status JOB_ID Query the status of a specific job ID. │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Input Files (provide --input-dir OR --fasta) ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --input-dir -i PATH Directory containing: `all_genome.fa`, ``, ``. Exclusive with `--fasta`. │
│ --fasta -fa PATH Input FASTA file (e.g., `all_genome.fa`). Alternative to `--input-dir`. │
│ --categories -c PATH Genome categories TSV file. Optional if using `--fasta`. Ignored if `--input-dir` is used (looks for `genome_categories.tsv` inside). │
│ --gene-bed -b PATH Gene BED file for SSR-gene analysis. Optional. If `--input-dir` is used, looks for `gene.bed` inside. │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Analysis Parameters ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --reference-id -ref TEXT Reference genome ID for comparative analysis. Optional parameter for reference-based comparisons. │
│ --output-dir -o DIRECTORY Base output directory for jobs. Overrides CROSSROAD_JOB_DIR env var. │
│ --flanks -f Process flanking regions. │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ PERF SSR Detection Parameters ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --mono INTEGER Mononucleotide repeat threshold. [default: 12] │
│ --di INTEGER Dinucleotide repeat threshold. [default: 6] │
│ --tri INTEGER Trinucleotide repeat threshold. [default: 4] │
│ --tetra INTEGER Tetranucleotide repeat threshold. [default: 3] │
│ --penta INTEGER Pentanucleotide repeat threshold. [default: 3] │
│ --hexa INTEGER Hexanucleotide repeat threshold. [default: 2] │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Filtering Parameters ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --min-len -l INTEGER Minimum genome length for filtering. [default: 1000] │
│ --max-len -L INTEGER Maximum genome length for filtering. [default: 10000000] │
│ --unfair -u INTEGER Maximum number of N's allowed per genome for Crossroad analysis. [default: 0] │
│ --repeat-threshold -rc INTEGER Repeat count Threshold for hotspot filtering (keeps records > this value). [default: 1] │
│ --genome-threshold -g INTEGER Genome count Threshold for hotspot filtering (keeps records > this value). [default: 2] │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Performance & Output ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --threads -t INTEGER Number of threads for Crossroad analysis. [default: 50] │
│ --plots -p Enable plot generation. │
│ --intrim-dir TEXT Name for the intermediate files directory (within the main job output dir). [default: intrim] │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯

(jitENV) hp@hp-HP-Z2-Tower-G9-Workstation-Desktop-PC:~/jitendraTEST$

(Deemed University)

Hamdard Nagar, New Delhi – 110 062

R E C R U I T M E N T

(Advertisement No. 5/2014)

Applications on prescribed form are invited for filling up the following teaching positions in the Department of Biotechnology, Faculty of Science in the university. Eligible candidates may apply on or before 30.09.2014.

1. Professor/Associate Professor - One in Pay Band of Rs. 37400-67000+ AGP Rs.10000/9000

2. Assistant Professor - Two in Pay Band of Rs. 15600-39100+ AGP Rs. 6000/-

ASSISTANT PROFESSOR – 02 (including 01 SFS)

Specialization : Bioinformatics

Qualification and Experience :

Ph.D. in Biotechnology or an allied discipline with M.Sc. in Biotechnology/ Biochemistry in the First division or equivalent grade from a recognized University/ Institute.

NET in Life Science or allied discipline in addition to the above qualification.

Experience : At least two years of Post-doctoral teaching and/or research experience in Bioinformatics or relevant field in a UGC recognized Institution of repute or international research institute/ University. Proof of research to be evidenced by publications in SCI-indexed journals of high impact factor as the first or corresponding author.

Note : University may consider exempting candidates from NET, who has been awarded Ph.D. degree from ‘A’ Grade accredited University following the procedure as notified by the UGC in its Regulations of 2009 and adopted by Jamia Hamdard.

For more information: http://www.jamiahamdard.ac.in/PDF/Online%20application%20form%20_Teaching_1.pdf
http://www.jamiahamdard.ac.in/PDF/PBAS.pdf

http://www.gigasciencejournal.com/content/2/1/10/abstract

http://blogs.nature.com/news/2013/07/genome-assembly-contest-prompts-soul-searching.html

http://assemblathon.org/post/44431915644/feedback-and-analysis-of-the-assemblathon-2-p