BOL: Related items

phyloXML: XML for evolutionary biology and comparative genomics

Jit — Sun, 08 Dec 2019 09:41:18 -0600

phyloXML (example) is an XML language designed to describe phylogenetic trees (or networks) and associated data. PhyloXML provides elements for commonly used features, such as taxonomic information, gene names and identifiers, branch lengths, support values, and gene duplication and speciation events. Using these standardized elements allows interoperability between various applications and databases. Furthermore, both due to extensible nature of XML itself and the provision of elements by phyloXML, extensibility as well as domain specific applications are ensured. The structure of phyloXML is described by XML Schema Definition (XSD) language.

http://www.phyloxml.org/archaeopteryx-js/adh.html

Address of the bookmark: http://www.phyloxml.org/

NGSymposium in Computational Biology

Mon, 09 Mar 2020 06:00:30 -0500

We have a great pleasure to invite you to the NGSymposium in Computational Biology to celebrate the 5th anniversary of the NGSchool Summer Schools. This international conference will make way for exchanging knowledge and experiences between experienced and early-stage researchers as well as bioinformaticians. The meeting will be held on 31.07 - 1.08.2020 in Warsaw. It will be a satellite event to the #NGSchool2020: Statistical Learning in Genomics. It will cover a wide range of topics from basic and applied biomedical sciences: bioinformatics, genomics, transcriptomics, computational biology, Machine Learning.

Registration of active participants will be open from February, 27 12 PM CET to April 17, 23:59 CET. In registration forms you will be asked for providing us with some basic information about yourself. You will also be able to submit your abstract. You can save your registration form after filling it partially and come back later to supply more data e.g. upload an abstract. Your registration will be completed only with the payment of the registration fee reaching our accounts - please make sure to transfer the money in advance!

Registration of passive participants will be open after closing of registration of active participants.

Details an registration: https://ngschool.eu/conference/

Breeding Insight

BioStar — Wed, 06 Jan 2021 19:49:21 -0600

Breeding Insight at Cornell University will leverage recent improvements in genomics and open source informatics components, and in partnership with small breeding programs, will enable these programs to harness powerful digital tools to accelerate their genetic gains

Breeding Insight is funded by the U.S. Department of Agriculture (USDA) Agricultural Research Service (ARS) through Cornell University. The USDA ARS delivers scientific solutions to national and global agricultural challenges. As a global leader in agricultural discovery through scientific excellence, ARS is committed to delivering cutting-edge, scientific tools and innovative solutions for American farmers, producers, industry, and communities to support the nourishment and well-being of all people; sustaining our nation’s agroecosystems and natural resources; and ensuring the economic competitiveness and excellence of our agriculture.

Address of the bookmark: https://www.breedinginsight.org/

The Day We Began Reading the DNA of the World

Jitendra Narayan — Sat, 05 Sep 2026 01:43:21 -0500

Picture waking up and knowing that in one lab, a scientist is reading the DNA of a whale. In another, a team is sequencing a rare plant. Meanwhile, researchers in India are decoding the genomes of different human populations.

Many organisms. Many countries. All share one remarkable goal: to understand the genetic story of life.

DNA is nature's instruction manual, written with just four letters: A, T, C, and G. For years, scientists could only read small sections of this huge book. Now, new sequencing technology lets us read entire genomes like never before.

One of the most ambitious projects is the Earth BioGenome Project (EBP). Its goal is to create reference genomes for about 1.5 million known eukaryotic species. This project links genome research across continents, species, and scientific fields.

But this story goes beyond just animals and plants.

A New Chapter in Human Genomics

Large human genome projects are changing how we understand our own genetic diversity.

India's GenomeIndia project has sequenced thousands of people from different populations. This work is uncovering genetic variation that global databases have often missed.

Similar population-scale effSimilar large-scale projects are happening worldwide. The All of Us Research Program in the United States, Europe's 1+ Million Genomes initiative, South Korea's national genomic data program, and projects in Saudi Arabia, Australia, and Singapore are all building huge genomic resources.collect DNA.

The real goal is to link genomes with health, disease, and other biological information. This creates a base for more accurate research and, in time, more personalized medicine.

A Race Against Time

There is also an important twist.

We are sequencing Earth's biodiversity even as many species face growing environmental threats.

A genome alone cannot save a species, but it does keep important information about its biology, evolution, and genetic diversity. This knowledge helps scientists understand risks, guide conservation, and find traits that could help agriculture or medicine.

Projects like the Darwin Tree of Life, which studies species in Britain and Ireland, and the African BioGenome Project, which is growing genomics work across Africa, are key parts of this worldwide effort.

Projects to Watch

Earth BioGenome Project (EBP) - A global effort to sequence and annotate roughly 1.5 million known eukaryotic species and create a comprehensive reference library of Earth's biodiversity.
Vertebrate Genomes Project (VGP) - Focuses on producing high-quality reference genomes for vertebrate species, providing a major foundation for the wider Tree of Life.
Darwin Tree of Life - A UK and Ireland initiative aiming to sequence approximately 70,000 species, creating a detailed genomic map of regional biodiversity.
African BioGenome Project (AfricaBP) - A pan-African initiative focused on sequencing Africa's biodiversity while strengthening genomics and bioinformatics capacity across the continent.
European Reference Genome Atlas (ERGA) - A European effort to generate high-quality reference genomes for Europe's biodiversity and connect national sequencing efforts.
Canada BioGenome Project - Building reference genomes for Canadian biodiversity, supporting conservation, research and the study of ecosystems.
California Conservation Genomics Project - Uses genomics to understand and protect California's biodiversity and help inform conservation decisions.
Bat1K - An ambitious global effort to sequence the genomes of all known bat species, helping scientists study their evolution, longevity, immunity and unique biology.
Bird 10,000 (B10K) - A global project aiming to create genome resources covering the world's bird diversity and reconstruct avian evolutionary history.
Global Invertebrate Genomics Alliance (GIGA) - Builds genomic resources for the enormous and genetically diverse world of invertebrates.
GenomeIndia - India's national human-genome initiative, designed to capture the country's extraordinary population diversity and create a reference resource for Indian genomics.
All of Us Research Program - A US national research program combining genomic information with health and lifestyle data at population scale.
1+ Million Genomes / Genome of Europe - A European effort to enable secure, cross-border use of genomic and health data and develop genome-scale resources involving more than one million people.
Korea National Integrated Bio Big Data Project - South Korea's large-scale national effort combining genomic and health information from a very large population cohort.
Saudi Genome Program - A national genomics initiative focused on genetic diseases, population genomics and precision medicine in Saudi Arabia.
Australian Genomics / Genomics Health Futures Mission - Australia's growing investment in genomic medicine, rare disease research and population-scale health genomics.

The Library of Life

The fuThe future of genomics is not just about sequencing one genome at a time. Now, it is about creating a worldwide network of genomes—human and non-human, individual and species—linked by powerful databases and advanced computational tools.ine a library without shelves.

In this library, the books are genomes. The pages are made of DNA. Scientists and machines are the readers. And this library is still being written. Each genome sequenced today adds a new page to the story of life and helps us better understand our place in it.

Pevzner Lab !

Thu, 02 Nov 2023 05:39:26 -0500

The laboratory works on genome sequencing, immunoproteogenomics, antibiotics sequencing, and comparative genomics - computational technologies that enabled new applications and allowed scientists to attack biological problems that remained beyond the reach of previous techniques.

https://bioalgorithms.ucsd.edu/research4.html

Detect the sequence pattern and its location in fasta file with match and mismatches information.

Jit — Thu, 26 Sep 2013 15:02:53 -0500

This script is one of my old script to detect some centromeric pattern in chromosomes. User can also control the number of mismatches allowed through command line ..

To run:

perl centro.pl

Free Books on Machine Learning and Artificial Intelligent !

BioStar — Thu, 16 Mar 2023 00:10:24 -0500

An Introduction to Statistical Learning
This book provides a broad and less technical treatment of key topics in statistical learning. Each chapter includes an R lab. This book is appropriate for anyone who wishes to use contemporary tools for data analysis.

https://hastie.su.domains/ISLR2/ISLRv2_website.pdf

Python Data Science Handbook
You’ll learn how to use the core libraries essential for working with data in Python: particularly IPython, NumPy, Pandas, Matplotlib, Scikit-Learn, and related packages. This resource is perfect for tackling day-to-day issues such as cleaning, manipulating, and transforming data — or building machine learning models.

https://jakevdp.github.io/PythonDataScienceHandbook/

Dive into Deep Learning
Interactive deep learning book with code, math, and discussions. Implemented with PyTorch, NumPy/MXNet, JAX, and TensorFlow. Adopted at 400 universities from 60 countries

https://d2l.ai/

Approaching (Almost) Any Machine Learning Problem
This book is for people who have some theoretical knowledge of machine learning and deep learning and want to dive into applied machine learning. The book is more oriented towards how and what should you use to solve machine learning and deep learning problems. The book is for you if you are looking for guidance on approaching machine learning problems.

https://github.com/abhishekkrthakur/approachingalmost/blob/master/AAAMLP.pdf

Fiona Brinkman Laboratory

Sun, 14 Jul 2013 12:46:31 -0500

Infectious disease control needs to be made more “sustainable”. We need to reduce selective pressure on pathogens to evolve antibiotic resistance. We need to control infectious disease outbreaks and associated immune disorders with a better understanding of the genetic, environmental and social factors that impact disease spread and severity.

Research Area

Investigating the role in disease of both the microbe and its host (i.e immune system failure), using genomics and systems biology-based approaches
Using genomics and network analysis to characterize disease outbreaks and their environmental/social/genetic causes, and
Identifying new anti-infective and immune modulating therapies/biomarkers.

Link @ http://www.brinkman.mbb.sfu.ca/

BioProgramming

Jitendra Narayan — Sun, 14 Jul 2013 16:29:53 -0500

The completion of the first human genome drafts was just a start of the modern DNA sequencing era which resulted in further invention, improved development toward new advanced strategies of high-throughput DNA sequencing, so called the “high-throughput next generation sequencing” (HT-NGS). The decreasing genome sequencing cost and desire to explore and understand biological machanism at genomic level, speed up the genomic sequencing projects. In the fast growing HT-NGS technologies, the main challenge is to cope with the analysis of vast production of sequencing database through advanced bioinformatics tools. In oder to develope sotware/tools bioinformatician/ biological programmers need to expertise in any one one the programming language. However, sometime one language are not enough to handle all sort of biological needs, which compel us to learn new biologically suitable language to handle ever growing genome or protein sequences.

The next step after reading genetic code is writing a script to analyse and explore the hidden information. This tutorial is aimed to introduce you new biological programming languages with their packages/libraries, and assist in your scripting work.

Navigate the sub-section of this page [ see right hand side of the page for it ]

Livestock Functional Genomics Summer School (LFG 2013)

Fri, 02 Aug 2013 09:57:37 -0500

*Livestock Functional Genomics Summer School - Call for applications*

1st Livestock Functional Genomics Summer School (LFG 2013).

This School was designed for graduate students and early-stage researchers with interest in livestock genomics, who are engaged in projects that require knowledge in the field of computational biology.

Sixty selected participants will spend 13 days receiving theoretical and practical training in genomic data handling from internationally renowned experts.

After the course, the participant should understand the basis and the context of livestock big molecular data, and be able to manipulate high density genotypes, whole genome sequences and transcriptome data.

The Summer School will be held in Araçatuba-SP Brazil, from the 13th to the 21st of September 2013.

All accepted participants will have *expenses fully covered (air ticket, hotel and meals)*, including a free pass to the 5th International Symposium on Animal Functional Genomics http://www.isafg2013.org.br

Applicants will be selected based on their résumés. Application date is due by August 10th. Results will be announced in August 12th.

Please consult website: http://www.sciencesatellite.org.br/sschool