BOL: Related items

Bioinformatics Trainee at University of Kalyani

Tue, 22 Dec 2015 01:51:42 -0600

Bioinformatics Trainee
Eligibility : MSc
Location : Kolkata
Last Date : 28 Dec 2015
Hiring Process : Walk - In
University of Kalyani

Bioinformatics Trainee Job position in University of Kalyani
Number of Posts : 02
Qualification : M.Sc. in any branch of life science with prior knowledge of Bioinformatics
Fellowship / Stipend / Salary : As per DBT rules
Duration of the Post : Six months starting from January, 2016
How to apply
Walk-in-interview will be held on 28.12.2015 at Department of Biochemistry and Biophysics, University of Kalyani.

More at http://www.klyuniv.ac.in/index.php/recruitments

List of visualization tools for network biology

Jit — Mon, 29 Jan 2018 05:12:24 -0600

Network analysis is any structured technique used to mathematically analyze a circuit (a “network” of interconnected components). The Network analysis provides the ability to quantify associations between individuals, which makes it possible to infer details about the network as a whole at the species and/or population level. Few tools published in BMC are listed here https://bmcbioinformatics.biomedcentral.com/articles/sections/networks-analysis.

Following are the list of standalone applications for network analysis:

Arena 3D

3D visualization of multi-layer networks

http://www.arena3d.org

Biana

Data integration and network management

http://sbi.imim.es/web/BIANA.php

BioLayout Express 3D

2D/3D network visualization

http://www.biolayout.org/

BiologicalNetworks

Efficient integrated multi-level analysis of microarray, sequence, regulatory and other data

http://www.biologicalnetworks.org

BioMiner

Modeling, analyzing and visualizing biochemical pathways and networks

http://www.zbi.uni-saarland.de/chair/projects/BioMiner

Cell Illustrator

Petri nets for modeling and simulating biological networks

http://www.cellillustrator.com

COPASI

Analysis of biochemical networks and their dynamics

http://www.copasi.org/

Cytoscape

Network visualization and analysis. Over 200 plugins [60]

http://www.cytoscape.org/

Dizzy

Chemical kinetics stochastic simulation software

http://magnet.systemsbiology.net/software/Dizzy/

DyCoNet

Gephi plugin that can be used to identify dynamic communities in networks

https://github.com/juliemkauffman/DyCoNet

GENeVis

Network and pathway visualization

http://tinyurl.com/genevis/

GEPHI

Interactive visualization and exploration for any network and complex system, dynamic and hierarchical graph.

https://gephi.org

Igraph

Collection of network analysis tools with the emphasis on efficiency, portability and ease of use

http://igraph.sourceforge.net

Medusa

Semantic and multi-edged simple networks

https://sites.google.com/site/medusa3visualization/

NAViGaTOR

Visualizing and analyzing protein-protein interaction networks

http://tinyurl.com/navigator1/

N-Browse

Interactive graphical browser for biological networks

http://www.gnetbrowse.org/

NeAT

Topological and clustering analysis of networks

http://rsat.ulb.ac.be/neat/

Ondex

Data integration and visualization of large networks

http://www.ondex.org/

Osprey

Visualization and annotation of biological networks

http://biodata.mshri.on.ca/osprey/servlet/Index

Pajek

Analysis and visualization of large networks and social network analysis

http://vlado.fmf.uni-lj.si/pub/networks/pajek/

PathwayAssist

Navigation and analysis of biological pathways, gene regulation networks and protein interaction maps.

http://www.ariadnegenomics.com/downloads/

PIVOT

Layout algorithms for visualizing protein interactions and families

http://acgt.cs.tau.ac.il/pivot/

ProCope

Prediction and evaluation of protein complexes from purification data experiments

http://www.bio.ifi.lmu.de/Complexes/ProCope/

ProViz

Visualization and exploration of interaction networks. Gene Ontology and PSI-MI formats supported

http://cbi.labri.fr/eng/proviz.htm

SpectralNET

Network analysis and visualizations. Scatter plots and dimensionality reduction algorithms

https://www.broadinstitute.org/software/spectralnet

Tulip

Enables the development of algorithms, visual encodings, interaction techniques, data models and domain-specific visualizations

http://tulip.labri.fr/TulipDrupal/

VANESA

Automatic reconstruction and analysis of biological networks and Petri nets based on life-science database information

http://agbi.techfak.uni-bielefeld.de/vanesa/

VANTED

Network reconstruction, data visualization, integration of various data types, network simulation

http://tinyurl.com/vanted/

yEd

Creation of diagrams manually and import external data

http://tinyurl.com/yEdGraph/

Web tools for network analysis

APID

Unified protein-protein interactions from BIND, BioGRID, DIP, HPRD, IntAct and MINT

http://bioinfow.dep.usal.es/apid/

Arcadia

Translates text-based descriptions of biological networks (SBML files) into standardized diagrams (Systems Biology Graphical Notation Process Description maps)

http://arcadiapathways.sourceforge.net/

AVIS

Viewer for signaling networks

http://actin.pharm.mssm.edu/AVIS2

bioPIXIE

Discovery of biological networks from diverse functional genomic data

http://pixie.princeton.edu/pixie

CellPublisher

Interactive representations of biochemical processes

http://cellpublisher.gobics.de/

Graphle

Distributed network exploration and visualization of interactive large, dense graphs

http://tinyurl.com/graphle/

GraphWeb

Web server for graph-based analysis of biological networks

http://biit.cs.ut.ee/graphweb/

Hubba

Web-based service to explore the essential nodes in a network

http://hub.iis.sinica.edu.tw/Hubba

NetworkBLAST

Analysis of protein interaction networks across species to infer protein complexes that are conserved in evolution

http://www.cs.tau.ac.il/~bnet/networkblast.htm

Pathview

Tool set for pathway-based data integration and visualization

http://Pathview.r-forge.r-project.org/

PINA

Integrated platform for protein interaction network construction, filtering, analysis, visualization and management

http://cbg.garvan.unsw.edu.au/pina/home.do

ReMatch

Web-based tool for integration of user-given stoichiometric metabolic models into a database collected from public data sources

http://www.cs.helsinki.fi/group/sysfys/software/rematch/

SNOW

Gene mapping on a reference or human protein-protein interaction network that SNOW hosts

http://snow.bioinfo.cipf.es

STITCH

Resource to explore known and predicted interactions of chemicals and proteins

http://stitch.embl.de/

STRING

Protein interaction networks and integration of data such as genomic context, high-throughput experiments, conserved coexpression and previous knowledge derived from the literature

http://string-db.org

TVNViewer

An interactive visualization tool for exploring networks that change over time or space

http://www.sailing.cs.cmu.edu/main/?page_id=545

tYNA

System for managing, comparing and mining multiple networks

http://tyna.gersteinlab.org/tyna/

VisANT

Visualization, mining, analysis and modeling of biological networks, metabolic networks and ecosystems

http://visant.bu.edu/

Chekulaevalab

Tue, 12 Jan 2016 02:32:03 -0600

Focusing on understanding the molecular mechanisms that regulate mRNA translation, localization and stability and role of non-coding RNAs in this process. Up to 90% of human DNA is estimated to be transcribed into so called non-coding RNAs that are not translated into proteins. Many of them act as potent modifiers of gene expression. miRNAs are a class of such short non-coding RNAs. They regulate expression of more than a half of eukaryotic genes, thus, affecting multiple biological processes, including cell proliferation, differentiation, apoptosis and senescence. Not surprisingly, miRNAs are involved in many human pathologies, including cancer and neurological disorders and hold great potential as drug targets, disease markers, as well as therapeutic agents.
Our lab is located at the Berlin Institute for Medical Systems Biology (BIMSB), a part of the Max Delbrück Center for Molecular Medicine (MDC).

http://www.chekulaevalab.org/

Bokeh: An interactive visualization library that targets modern web browsers for presentation

Jit — Fri, 10 Aug 2018 18:43:08 -0500

Bokeh is an interactive visualization library that targets modern web browsers for presentation. Its goal is to provide elegant, concise construction of versatile graphics, and to extend this capability with high-performance interactivity over very large or streaming datasets. Bokeh can help anyone who would like to quickly and easily create interactive plots, dashboards, and data applications.

To get started using Bokeh to make your visualizations, see the User Guide.

To see examples of how you might use Bokeh with your own data, check out the Gallery.

A complete API reference of Bokeh is at Reference Guide.

If you are interested in contributing to Bokeh, or extending the library, see the Developer Guide.

Address of the bookmark: https://bokeh.pydata.org/en/latest/

RA at University of Pune

Mon, 07 Mar 2016 03:48:33 -0600

Research Associate Job vacancies in University of Pune on temporary basis

No. of Post : 01

Department : Science and Technology

Qualifications : Ph.D. with specialization in Bioinformatics/Machine Learning/ Mathematical Biology/ Computational Biology/ Systems Biology with a minimum of 55% marks in M. Sc. (50% for candidates belongs to reserved category) or equivalent grade. Candidates who have submitted their Ph.D. thesis and are waiting for award of Ph.D. are also eligible. OR M. Sc. Bioinformatics with two years of research experience in the areas mentioned above, a minimum of 55% marks in M.Sc. (50% for candidates belongs to reserved categories) or equivalent grade and at least one publication in Science Citation Index (SCI) journal. Preference will be given to B.I.N.C. /J.R.F. /N.E.T. /S.E.T. qualified candidates.

Emoluments : Rs. 20,000/- (Including H.R.A.) per month.
How to apply

The complete application along with necessary documents and certificates should reach to 'The Director, Bioinformatics Centre, Savitribai Phule Pune University (Formerly University of Pune), Caneshkhind Road. Pune - 411 007 on or before 21st March, 2016 within official hours except Sundays (i.e. 10.20 am to 06.00 pm).

More at http://collegecirculars.unipune.ac.in/sites/documents/Job%20Openings/Forms/AllItems.aspx

Environment for Tree Exploration (ETE) is a Python programming toolkit that assists in the recontruction, manipulation, analysis and visualization of phylogenetic trees

Rahul Nayak — Wed, 27 Nov 2019 05:32:33 -0600

The Environment for Tree Exploration (ETE) is a Python programming toolkit that assists in the recontruction, manipulation, analysis and visualization of phylogenetic trees (although clustering trees or any other tree-like data structure are also supported).

Other tools

https://github.com/shenwei356/taxonkit

ETE, version: 3.1.1
BioPython, version: 1.73
taxadb, version: 0.10.1
TaxonKit, version: 0.5.0

Address of the bookmark: https://pypi.org/project/ete3/3.1.1/

Tools for Geospatial data analysis !

BioStar — Wed, 22 Mar 2023 02:10:28 -0500

Geospatial data is becoming increasingly important in many fields, including urban planning, environmental science, public health, and more. These tools can help you work with data from a variety of sources, including satellite imagery, GPS data, and other forms of spatial data. They can help you visualize data, perform complex analysis, and even create maps and other visualizations.

The list includes some of the most popular and widely used geospatial tools available in Python. These tools can help you work with data from a variety of sources and in a variety of formats. Some of the tools are focused on visualization, such as Cartopy, Folium, and Contextily, which allow you to create interactive maps and other visualizations. Other tools are more focused on data manipulation and analysis, such as Fiona, GeoPandas, and Rasterio, which allow you to manipulate and analyze spatial data in a variety of ways.

The list also includes some tools for working with specific types of geospatial data. For example, the H3 library is designed specifically for working with hexagonal grids, while PySAL is focused on spatial econometrics and spatial analysis. Whether you are a data scientist, GIS specialist, or geospatial enthusiast, these tools are sure to enhance your work and help you achieve your goals.

In summary, this list is an excellent resource for anyone working with geospatial data in Python. It contains a wide range of tools for working with different types of data, and can help you visualize data, perform complex analysis, and create maps and other visualizations. If you're looking to enhance your skills in geospatial analysis, this list is definitely worth checking out.

These tools are:

ArcGIS - https://lnkd.in/dgC6sKJH
Cartopy - https://lnkd.in/dc8ijXRg
Contextily - https://lnkd.in/dTdQsmKX
Descartes - https://lnkd.in/dCJykxwW
Fiona - https://lnkd.in/d8sJ3Q5a
Folium - https://lnkd.in/dfSsE-MB
GDAL - https://lnkd.in/dYBJBaAY
Geohash - https://lnkd.in/d_NxJ4_M
GeoJSON - https://lnkd.in/daGs2WYq
GeoPandas - https://lnkd.in/dBTFKKV3
Geopy - https://lnkd.in/dfAzR8Xa
Gevent - http://www.gevent.org
H3 - https://h3geo.org/docs/
OSMnx - https://lnkd.in/dm3pHgUS
PyQGIS - https://lnkd.in/dShWyWVr
PySAL - https://pysal.org
Pydeck - https://lnkd.in/dGBFu-iw
Pyproj - https://lnkd.in/dNG9fdkm
RTree - https://lnkd.in/dURMiYpU
Rasterio - https://lnkd.in/dEMC6ve6
Scikit-mobility - https://lnkd.in/dpHhaX2J
Shapely - https://lnkd.in/d568datK

These tools offer a wide range of capabilities for working with geospatial data, from visualizing and manipulating data to performing complex analysis and modeling. Whether you are a data scientist, GIS specialist, or geospatial enthusiast, these tools are sure to enhance your work and help you achieve your goals.

GenoFig: a user-friendly application for the visualization and comparison of genomic regions

BioStar — Mon, 05 Aug 2024 23:06:58 -0500

Tool for graphical vizualisation of annotated genetic regions, and homologous regions comparison. It is an independent recoding of Easyfig 2 initially developped by at the S. Beatson Lab [https://mjsull.github.io/Easyfig/]

Download the GenoFig source code using the 'Download' button on top of this page. Cloning is currently not available for people not member of the INRAE French Institution. After decompression, open a terminal in the folder containing the decompressed files and run:

conda env create -f extras/requirements.yml
extras/SETUP.sh

Address of the bookmark: https://forgemia.inra.fr/public-pgba/genofig

Project Fellow Bioinformatics at Central University of Himachal Pradesh

Tue, 09 Feb 2016 03:58:00 -0600

Project Fellow Bioinformatics

Eligibility : MSc(Bio-Chemistry, Bio-Informatics)

Location : Kulu

Last Date : 07 Mar 2016

Hiring Process : Face to Face Interview
Central University of Himachal Pradesh

Project Fellow Bioinformatics Job in Central University of Himachal Pradesh

Project (MRP) entitled: “A project proposal on targeting novel prokaryotic ubiquitin like post-translational modification pathway for therapeutic interventions against Mycobacterium tuberculosis” (No. MRP-MAJOR-MICR-2013-26840)

Essential Qualification: 1. Master degree in Bioinformatics/Biochemistry/Biotechnology/Environmental Science/Microbiology or any branch of Life Sciences with a minimum of 55% marks for general category (50% in case of SC/ST/PH) 2. UGC/CSIR NET, GATE qualified candidates will be given preference. Desirable Qualification: Experience in basic Bioinformatics and Molecular Biology techniques.

Age: Below 40 years as on 01/10/2015.

No.of Post: 1

Salary: NET/GATE qualified candidate: Rs. 16,000/-p.m. for initial two years and Rs. 18,000/- p.m. for the third year. Non-NET/GATE candidates: Rs. 14,000/-p.m. for initial two years and Rs. 16,000/-p.m. for the third year.

Mode of Selection: The selection shall be made on the basis of merit. The eligible candidates are required to appear for interview before the duly constituted Selection Committee for the purpose. The scheduled date, time and venue for the interview shall be intimated to the eligible candidates through phone/ e-mail.
How to apply

Last date for the receipt of applications is 07.03.2016.

More at http://www.cuhimachal.ac.in/news_all.aspx

Centurion

Jit — Fri, 12 Feb 2016 04:45:41 -0600

Although centromeres are essential for life and are the subject of extensive research, centromere locations in yeast genomes are difficult to infer, and in most species they are still unknown. Recently, the chromatin conformation assay Hi-C has been re-purposed for diverse applications, including de novo genome assembly, deconvolution of metagenomic samples, and inference of centromere locations. We describe a method, Centurion, that jointly infers the locations of all centromeres in a single yeast genome by exploiting the centromeres’ tendency to cluster in 3D space. We first demonstrate the accuracy of Centurion in identifying known centromere locations from high coverage Hi-C data of budding yeast and a human malaria parasite. We then use two metagenomic samples with relatively low coverage Hi-C data to infer centromere locations for each chromosome in 14 different yeast species. For yeasts with large centromeres (e.g., S. pombe) Centurion predicts the exact centromere locations. For seven yeasts with point centromeres, Centurion predicts most of the centromeres at an average of 5~kb distance from their known locations. Finally, we predict centromere coordinates for six yeast species that currently lack centromere annotations. These results suggest that Centurion can be used for centromere identification for a large number of yeast species, even with a limited amount of Hi-C sequencing.

Paper:http://www.ncbi.nlm.nih.gov/pubmed/25940625

More at http://cbio.ensmp.fr/centurion/

Address of the bookmark: http://cbio.ensmp.fr/centurion/