<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/43362?offset=10 https://bioinformaticsonline.com/bookmarks/view/40591/modelstudio-a-package-automates-the-explanation-of-machine-learning-predictive-models Wed, 22 Jan 2020 23:58:11 -0600 https://bioinformaticsonline.com/bookmarks/view/40591/modelstudio-a-package-automates-the-explanation-of-machine-learning-predictive-models <![CDATA[modelStudio: a package automates the explanation of machine learning predictive models]]> The modelStudio package automates the explanation of machine learning predictive models. This package generates advanced interactive and animated model explanations in the form of a serverless HTML site.

It combines R with D3.js to produce plots and descriptions for various local and global explanations. Tools for model exploration unite with tools for EDA (Exploratory Data Analysis) to give a broad overview of the model behavior. modelStudio is a fast and condensed way to get all the answers without much effort. Break down your model and look into its ingredients with only a few lines of code.

Address of the bookmark: https://modeloriented.github.io/modelStudio/index.html

]]> Jit https://bioinformaticsonline.com/bookmarks/view/43877/crowdgo-machine-learning-and-semantic-similarity-guided-consensus-gene-ontology-annotation Thu, 26 May 2022 00:59:49 -0500 https://bioinformaticsonline.com/bookmarks/view/43877/crowdgo-machine-learning-and-semantic-similarity-guided-consensus-gene-ontology-annotation <![CDATA[CrowdGO: Machine learning and semantic similarity guided consensus Gene Ontology annotation]]> CrowdGO is a protein Gene Ontology predictor using a meta approach, analyzing the predictions of other tools in order to get an improved precision and recall.

Please note that the CrowdGO snakemake workflow is currently only tested on Ubuntu. It should work on OSX, but please report any errors to maarten.reijnders@unil.ch or create an issue.

https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010075

Address of the bookmark: https://gitlab.com/mreijnders/crowdgo

]]> Shruti Paniwala https://bioinformaticsonline.com/opportunity/view/43227/project-associate-i-project-associate-ii-senior-project-associate-igib Thu, 05 Aug 2021 16:11:32 -0500 <![CDATA[Project Associate-I | Project Associate-II | Senior Project Associate @ IGIB]]> Experience in Next Generation Sequencing (NGS) application and interest in Genomics/ Clinical / Translational Applications. OR Good computational programming skills and deep interest in working on interface of Genomics and Clinical application.

Project Scientist-I
Experimental / Computation analysis experience in highthroughput genomics/ clinical application.

Project Manager
Experience in handling large biological projects involving high-throughput genomics/ clinical application.

Scientific Administrative Assistant
Lab Work.

More at https://vinodscaria.genomes.in/positionsopen

]]> https://bioinformaticsonline.com/bookmarks/view/34477/computational-genomics-applied-comparative-genomics Wed, 29 Nov 2017 05:11:30 -0600 https://bioinformaticsonline.com/bookmarks/view/34477/computational-genomics-applied-comparative-genomics <![CDATA[Computational Genomics: Applied Comparative Genomics]]> The primary goal of the course is for students to be grounded in theory and leave the course empowered to conduct independent genomic analyses. We will study the leading computational and quantitative approaches for comparing and analyzing genomes starting from raw sequencing data. The course will focus on human genomics and human medical applications, but the techniques will be broadly applicable across the tree of life. The topics will include genome assembly & comparative genomics, variant identification & analysis, gene expression & regulation, personal genome analysis, and cancer genomics. The grading will be based on assignments, a midterm exam, class presentations, and a significant class project. There are no formal course prerequisites, although the course will require familiarity with UNIX scripting and/or programming to complete the assignments and course project.

Address of the bookmark: https://github.com/schatzlab/appliedgenomics

]]> Jit https://bioinformaticsonline.com/bookmarks/view/43369/a-guide-to-machine-learning-for-biologists Wed, 15 Sep 2021 13:21:08 -0500 https://bioinformaticsonline.com/bookmarks/view/43369/a-guide-to-machine-learning-for-biologists <![CDATA[A guide to machine learning for biologists]]> We aim to provide readers with a gentle introduction to a few key machine learning techniques, including the most recently developed and widely used techniques involving deep neural networks. We describe how different techniques may be suited to specific types of biological data, and also discuss some best practices and points to consider when one is embarking on experiments involving machine learning. Some emerging directions in machine learning methodology are also discussed.

Address of the bookmark: https://www.nature.com/articles/s41580-021-00407-0

]]> LEGE https://bioinformaticsonline.com/file/view/4882/detect-the-sequence-pattern-and-its-location-in-fasta-file-with-match-and-mismatches-information Thu, 26 Sep 2013 15:02:53 -0500 https://bioinformaticsonline.com/file/view/4882/detect-the-sequence-pattern-and-its-location-in-fasta-file-with-match-and-mismatches-information <![CDATA[Detect the sequence pattern and its location in fasta file with match and mismatches information.]]> 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

]]> Jit https://bioinformaticsonline.com/researchlabs/view/856/papenfuss-lab Sun, 14 Jul 2013 12:22:28 -0500 <![CDATA[Papenfuss Lab]]> The human genome project and similar projects in disease-causing organisms such as Plasmodium falciparum, which causes malaria in humans, have provided new tools for discovery in biology and have accelerated the development of understanding in human disease.

Research Area:
Analysis of Next Generation sequence data in cancer
Methods for analysis of structural variation in cancer genomes
Next Generation sequencing in malaria
Computational comparative genomics
Sensitive genomic sequence search techniques using hidden Markov models
Tasmanian devil facial tumour disease

Link @ http://www.wehi.edu.au/faculty_members/dr_tony_papenfuss

]]> https://bioinformaticsonline.com/opportunity/view/869/bioinformatics-phd-studentship-available-in-new-zealand Sun, 14 Jul 2013 13:36:30 -0500 <![CDATA[Bioinformatics PhD studentship available in New Zealand]]> Bioinformatics PhD studentship available in New Zealand

The importance of transcriptional control has been explored in a burgeoning line of research over several decades; nevertheless, we are still far from having a complete picture of the regulatory mechanisms of genes and non-coding RNAs, and their influences on different phenotypes and disease states of a cell. Recent shifts towards large-scale analyses of transcriptional regulation on a sequence and epigenetic level are at the forefront of research, mainly due to sequencing technology advancements and a deeper understanding of the fundamental regulatory processes involved.

Arriving at a better understanding of the influence of specific parts of the overall regulatory machinery on disease states is a high priority of the group’s research agenda.

We are seeking an enthusiastic student to join the group as a PhD student. Applicants must have a BSc(Hons) or MSc degree in a relevant discipline and a willingness to learn and apply new techniques and work in a team. Both local and international students are encouraged to apply.

The studentship covers all university fees and an annual tax-exempt stipend of NZ$22,000 for three years.

Sebastian Schmeier recently joined Massey University and started his own research group in Auckland, New Zealand, a city regularly ranked one of the most livable in the world. This is your chance to experience the amazing Auckland lifestyle and the excitement of joining a young new science team, while staying connected to world class scientific networks.

To apply for the post, please send a cover letter stating your interest in the position and why you think you would be a good candidate, a Curriculum Vitae, a copy of your academic transcript, a sample of your written scientific work, and the names of three referees. Applications will be accepted until the position is filled.

Enquiries and applications to Sebastian Schmeier (s.schmeier@massey.ac.nz).

]]> https://bioinformaticsonline.com/pages/view/923/phylogenetic-for-bioinformatics Tue, 16 Jul 2013 03:50:30 -0500 https://bioinformaticsonline.com/pages/view/923/phylogenetic-for-bioinformatics <![CDATA[Phylogenetic for Bioinformatics]]> Biologists estimate that there are about 5 to 100 million species of organisms living on Earth today. Evidence from morphological, biochemical, and gene sequence data suggests that all organisms on Earth are genetically related, and the genealogical relationships of living things can be represented by a vast evolutionary tree, the Tree of Life. The Tree of Life then represents the phylogeny of organisms, i. e., the history of organismal lineages as they change through time.
Every living organism contains DNA, RNA, and proteins. Closely related organisms generally have a high degree of agreement in the molecular structure of these substances, while the molecules of organisms distantly related usually show a pattern of dissimilarity. Molecular phylogeny uses such data to build a "relationship tree" that shows the probable evolution of various organisms. Not until recent decades, however, has it been possible to isolate and identify these molecular structures. 
phylogenetics is the study of evolutionary relatedness among various groups of organisms (for example, species or populations), which is discovered through molecular sequencing data and morphological data matrices. In other word, Phylogenetics, the science of phylogeny, is one part of the larger field of systematics, which also includes taxonomy. Taxonomy is the science of naming and classifying the diversity of organisms Molecular phylogeny is the use of the structure of molecules to gain information on an organism's evolutionary relationships. The result of a molecular phylogenetic analysis is expressed in a so-called phylogenetic tree.

The evolutionary connections between organisms are represented graphically through phylogenetic trees. Due to the fact that evolution takes place over long periods of time that cannot be observed directly, biologists must reconstruct phylogenies by inferring the evolutionary relationships among present-day organisms. 
Application of the techniques that make this possible can be seen in the very limited field of human genetics, such as the ever more popular use of genetic testing to determine a child's paternity, as well as the emergence of a new branch of criminal forensics focused on genetic evidence.
The effect on traditional scientific classification schemes in the biological sciences has been dramatic as well. Work that was once immensely labor- and materials-intensive can now be done quickly and easily, leading to yet another source of information becoming available for systematic and taxonomic appraisal. This particular kind of data has become so popular that taxonomical schemes based solely on molecular data may be encountered. Proponents even claim that taxonomy was previously based on morphology alone, which of course is utter fable.

For additional information on phylogenetics, see list of Phylogenetics Resources on the Internet.

Phylogeny and Reconstructing Phylogenetic Trees: http://aleph0.clarku.edu/~djoyce/java/Phyltree/cover.html
the CBRG and Department of Statistics Phylogeny tutorial: http://www.compbio.ox.ac.uk/tutorials/phylogeny/
TUTORIAL: PHYLOGENETIC ANALYSIS USING PARSIMONY:http://home.cc.umanitoba.ca/~psgendb/GDE/phylogeny/parsimony/phylip.parsimony.html

PHYLIP: http://www.umanitoba.ca/afs/plant_science/psgendb/doc/Phylip/main.html
An Introduction to Molecular Phylogeny: http://bibiserv.techfak.uni-bielefeld.de/gcb04/tutorials/hoef-emden/GCB04Tut.pdf

How to make a phylogenetic tree: http://www.hiv.lanl.gov/content/sequence/TUTORIALS/TREE_TUTORIAL/Treetutorial.html
Phylogenetic Trees: http://cnx.org/content/m11052/latest/
Phylogeny by Ron Shamir: http://www.cs.tau.ac.il/~rshamir/algmb/01/scribe08/lec08.pdf
Introduction to Phylogeny: http://www.utm.edu/departments/cens/biology/rirwin/391/391Phylog.htm
Lecturer notes on Phylogeny: http://www.sbc.su.se/~bens/course_material/phylocourse1/lecture2.pdf
Principles and Practice of Phylogenetic Systematics:http://www.faculty.biol.ttu.edu/Strauss/Phylogenetics/LectureNotes.htm

Inferring phylogenetic trees: http://www.cis.hut.fi/Opinnot/T-61.6070/slides2008/pres_6070.pdf

Lecture Notes

Chapter 1 - The Diversity, Classification, and Evolution of Vertebrates:http://academic.emporia.edu/mooredwi/nathist/chap1.htm

Algorithms for Phylogenetic Reconstructions:http://lectures.molgen.mpg.de/Algorithmische_Bioinformatik_WS0405/phylogeny_script.pdf

Phylogeny.fr is a free, simple to use web service dedicated to reconstructing and analysing phylogenetic relationships between molecular sequences. Phylogeny.fr runs and connects various bioinformatics programs to reconstruct a robust phylogenetic tree from a set of sequences. For more detail : http://www.phylogeny.fr/version2_cgi/index.cgi

A Brief Tutorial on Phylogenetics
http://bioss.ac.uk/~dirk/talks/tutorial_phylogenetics.pdf

A Brief Tutorial on Phylogenetics Human Rabbit Chicken
http://bioss.ac.uk/~dirk/talks/psnup_tutorial_phylogenetics.pdf

Phylogenetic Tree Computation Tutorial Overview
http://pga.lbl.gov/Workshop/April2002/lectures/Olken.pdf

MrBayes: A program for the Bayesian inference of phylogeny
http://golab.unl.edu/teaching/SBseminar/manual.pdf

Web sites providing software for the construction of phylogenetic trees

  • TNT-Tree Analysis Using New Technology
  • Tree View-Taxonomy and Systematics Group at Glasgow
]]> Jitendra Narayan https://bioinformaticsonline.com/news/view/1469/prime-minister%E2%80%99s-100k-genome-project Thu, 08 Aug 2013 09:40:39 -0500 https://bioinformaticsonline.com/news/view/1469/prime-minister%E2%80%99s-100k-genome-project <![CDATA[Prime Minister’s 100k Genome Project]]> Genomics Ebgland is destined to sequence 100,000 patients over the next five year in England.  A landmark project by british government.

Genomics England will play a key role in building on the UK’s long track record as leader in medical science advances to push the boundaries by unlocking the power of DNA data. The UK will become the first ever country to introduce this technology in its mainstream health system – leading the global race for better tests, better drugs and above all better, more personalised care.

http://www.genomicsengland.co.uk/100k-genome-project/

]]> Jitendra Narayan