BOL: Related items

BioCodes/BioScripts

Jit — Tue, 22 Apr 2014 20:53:33 -0500

Over the years most bioinformatics people amass a collection of small utility scripts which make their lives easier. Too often they are kept either in private repositories or as part of a public collection to which noone else can contribute. Biocode is a curated repository of general-use utility scripts.

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

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

Epiviz: an interactive visualization tool for functional genomics data.

Jit — Mon, 09 Jul 2018 05:27:39 -0500

Epiviz is an interactive visualization tool for functional genomics data. It supports genome navigation like other genome browsers, but allows multiple visualizations of data within genomic regions using scatterplots, heatmaps and other user-supplied visualizations. It also includes data from the Gene Expression Barcode project for transcriptome visualization. It has a flexible plugin framework so users can addd3 visualizations. You can see a video tour here.

https://bioconductor.org/packages/release/bioc/html/epivizr.html

https://github.com/epiviz

https://github.com/epiviz/epiviz

Address of the bookmark: https://epiviz.github.io/

RA at ALAGAPPA UNIVERSITY

Sun, 04 May 2014 23:33:15 -0500

DEPARTMENT OF BIOTECHNOLOGY
(UGC SAP and DST-FIST & PURSE Sponsored Department)
ALAGAPPA UNIVERSITY
(A State University Accredited by NAAC with „A‟ Grade)
Karaikudi - 630 004, India

WALK IN INTERVIEW

A walk-in Interview for the following position tenable at the Bioinformatics Infrastructure Facility (BIF), Department of Biotechnology, Alagappa University will be held at the Department of Biotechnology, Alagappa University, Karaikudi 630 003 on 15.05.2014 (Thursday) at 01:00 PM. This national facility is funded by the Department of Biotechnology, Ministry of Science and Technology, Government of India, New Delhi. The main objectives of the Centre involve teaching and research activities in bioinformatics/biotechnology.

RA (One Post):

Salary : Rs. 11000 p.m. plus admissible HRA

Qualification: M.Sc., in Bioinformatics/Biotechnology/Biophysics/Biochemistry/ Life Sciences

Interested candidates are encouraged to send their Curriculum Vitae by email to “sk_pandian@rediffmail.com” in advance. On the day of interview, the candidates must produce original certificates in proof of their educational qualification and experience and a recommendation letter from the Head of the Department/Institution where last studied/worked. Candidates who have already passed the required Degree alone are eligible to appear for interview. No TA&DA will be given for attending the interview.

Advertisement: http://www.alagappabiotech.org/Walk%20in%20interview.pdf

Mulan: Multiple-sequence local alignment and visualization for studying function and evolution

Jit — Fri, 24 Aug 2018 09:50:01 -0500

Mulan: Multiple-sequence local alignment and visualization for studying function and evolution

Mulan (http://mulan.dcode.org/), a novel method and a network server for comparing multiple draft and finished-quality sequences to identify functional elements conserved over evolutionary time. Mulan brings together several novel algorithms: the TBA multi-aligner program for rapid identification of local sequence conservation, and the multiTF program for detecting evolutionarily conserved transcription factor binding sites in multiple alignments. In addition, Mulan supports two-way communication with the GALA database; alignments of multiple species dynamically generated in GALA can be viewed in Mulan, and conserved transcription factor binding sites identified with Mulan/multiTF can be integrated and overlaid with extensive genome annotation data using GALA.

Address of the bookmark: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC540288/

Associate Professor - Bio-Informatics at University of Allahabad in Allahabad

Wed, 07 May 2014 00:26:53 -0500

No of vacancies: 01

Pay scale: Pay Band of Rs. 37400-67000 with AGP of Rs. 9000.

i. Educational Qualification: Good academic record with a Ph.D. Degree in the concerned/allied/relevant disciplines.

ii. A Master's Degree with at least 55% marks (or an equivalent grade in a point scale wherever grading system is followed).

iii. A minimum of eight years of experience of teaching and/or research in an academic/research position equivalent to that of Assistant Professor in a University, College or Accredited Research Institution/industry excluding the period of Ph.D. research with evidence of published work and a minimum of 5 publications as books and/or research/policy papers.

iv. Contribution to educational innovation, design of new curricula and courses, and technology - mediated teaching learning process with evidence of having guided doctoral candidates and research students.

v. A minimum score as stipulated in the Academic Performance Indicator (API) based Performance Based Appraisal System (PBAS), set out in UGC Regulation.

Download application form from website: http://www.allduniv.ac.in/

Send your application to the Registrar, University of Allahabad, Allahabad-211002 (U.P.) on or before 30th April 2014

For more details: http://www.allduniv.ac.in/images/adv/backlog/advt-details.pdf OR http://www.allduniv.ac.in/images/news/extension-notice.pdf

Last Apply Date: 30 May 2014

GfaViz: flexible and interactive visualization of GFA sequence graphs

Jit — Thu, 23 Jan 2020 07:33:46 -0600

GFA (Graphical Fragment Assembly) is an emerging standard format for representing sequence graphs. Although it was originally conceived as a format for sequence assembly (hence the name), and this remains its core application, it is more general, and able to represent many different types of sequence graphs, including scaffolding graphs, alignment graphs, variant graphs and splicing graphs.

Address of the bookmark: https://github.com/ggonnella/gfaviz

DNA Replication Process [3D Animation]

Sat, 10 May 2014 04:41:22 -0500

See an organised list of all the animations: http://doctorprodigious.wordpress.com/hd-animations/

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.

Bioinformatics PhD at CUK Kerala

Sat, 10 May 2014 20:21:22 -0500

Applications are invited from highly motivated students (UGC-CSIR-JRF) with a background in Genomics/ Biotechnology/ Molecular Microbiology/ Biochemistry and Bioinformatics to pursue research leading to Ph.D. in the following areas;

1. Cancer Genomics

2. Microbial Genetics and Metagenomics

3. Human Infective Diseases

4. Computational Drug Design

Interested candidates may apply to Dr. Ranjith N. Kumavath, Assistant Professor & Head, Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Padannakad (PO), Nileshwar, Kasaragod-671328,Kerala. Email: RNkumavath@gmail.com

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