<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/27104?offset=610 https://bioinformaticsonline.com/bookmarks/view/43364/ragtag-a-collection-of-software-tools-for-scaffolding-and-improving-modern-genome-assemblies Sat, 11 Sep 2021 00:28:14 -0500 https://bioinformaticsonline.com/bookmarks/view/43364/ragtag-a-collection-of-software-tools-for-scaffolding-and-improving-modern-genome-assemblies <![CDATA[RagTag: a collection of software tools for scaffolding and improving modern genome assemblies]]> RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. Tasks include:

Address of the bookmark: https://github.com/malonge/RagTag

]]> Jit https://bioinformaticsonline.com/opportunity/view/11656/faculty-post-at-zhejiang-university Tue, 10 Jun 2014 03:40:40 -0500 <![CDATA[Faculty post at Zhejiang University]]> Zhejiang University (ZJU) is seeking faculty candidates for its newly launched, highly competitive and well funded “Hundred Talents Program”. This search covers all colleges and departments at ZJU. Applicants, expected to be about 35 years old, should hold PhD degree, and postdoctoral experiences are preferred for applicants in most fields. Applicants should have demonstrated commitment to excellence in teaching and research at a level comparable to the academic achievement of assistant professor or associate professor in world-renowned universities. Successful candidates must work full-time and are expected to establish internationally competitive and independent research program in cutting-edge areas of the relevant field at ZJU.

As one of the leading research-intensive universities in China, ZJU is located in the beautiful city of Hangzhou. Successful candidates will be employed as Principal Investigators and are qualified to supervise doctoral students. ZJU will offer an internationally competitive salary and the opportunity to purchase university's apartment at a price much lower than the market price, and will provide office and laboratory spaces as well as internationally competitive research startup packages.

Qualified applicants are strongly encouraged to submit their applications electronically to tr@zju.edu.cn. Applicants should include the following materials in pdf format: a comprehensive CV, a statement of research and teaching plan, and a list of 3 to 5 references with detailed contact information.

Contact：Talents Office, ZJU

Tel：+86-571-88981345, +86-571-88981390

Fax：+86-571-88981976

E-mail:tr@zju.edu.cn

]]> 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/blog/view/11592/xampp-starting-apache-fail-ubuntu Sat, 07 Jun 2014 05:52:35 -0500 https://bioinformaticsonline.com/blog/view/11592/xampp-starting-apache-fail-ubuntu <![CDATA[XAMPP: Starting Apache fail Ubuntu]]> Once you install XAMMP on linux, the most common problem you face is Apache failure. To fix the issues please use following command to first stop and then again start it.

sudo /etc/init.d/apache2 stop

sudo /etc/init.d/mysql stop

sudo /etc/init.d/proftpd stop

sudo /opt/lampp/lampp start

 

PhpMyAdmin “Wrong permissions on configuration file, should not be world writable!”

Once the Xammp is installed, it might be possible to set up the configuration file in writable mode. Try the following steps:

Just chmod 0755 the file

sudo chmod 0755 config.inc.php
]]> Ram Yash Pal https://bioinformaticsonline.com/bookmarks/view/4037/perl-and-bioperl-tutorials Wed, 28 Aug 2013 05:51:38 -0500 https://bioinformaticsonline.com/bookmarks/view/4037/perl-and-bioperl-tutorials <![CDATA[Perl and BioPerl Tutorials]]> This bookmark is created to store the useful Perl and BioPerl tutorial links at one place. Feel free to share and add more useful tutorial links here .... 

 

Address of the bookmark: http://cbb.sjtu.edu.cn/course/database/beginning.pdf

]]> Jitendra Narayan https://bioinformaticsonline.com/bookmarks/view/44200/dashboard-designing-tutorial Thu, 02 Mar 2023 06:48:43 -0600 https://bioinformaticsonline.com/bookmarks/view/44200/dashboard-designing-tutorial <![CDATA[Dashboard designing tutorial !]]> Dashboard Design Tutorial

Address of the bookmark: https://github.com/dthill196/SARS-2-Dashboard-Tutorial

]]> BioStar https://bioinformaticsonline.com/opportunity/view/12594/faculty-positions-at-central-university-of-punjab Mon, 07 Jul 2014 23:33:33 -0500 <![CDATA[Faculty Positions at Central University of Punjab]]> Faculty Positions: Rolling/Open Advertisement Advt.No: T-10 (2013)

Pay Scale: Pay Band Rs.15600-39100 with AGP of Rs.6,000/-

Essential Qualifications for Professors, Associate Professors, and Assistant Professors: As per “UGC REGULATIONS ON MINIMUM QUALIFICATIONS FOR APPOINTMENT OF TEACHERS AND OTHER ACADEMIC STAFF IN UNIVERSITIES AND COLLEGES AND MEASURES FOR THE MAINTENANCE OF STANDARDS IN HIGHER EDUCATION 2010“ and the 2nd Amendments to the regulation issued in June 2013.

For details: http://www.ugc.ac.in/oldpdf/regulations/revised_finalugcregulationfinal10.pdf http://www.ugc.ac.in/pdfnews/8539300_English.pdf and University rules.

Procedure to apply:

Application forms along with API form complete in all respect along with necessary documents and application fee of Rs. 500/-. (Rs. 250/- for Scheduled Caste/Scheduled Tribe/Person with disabilities) should be sent to:

Registrar, Central University of Punjab, City Campus, Mansa Road, Bathinda-151001

For more info visit: http://www.centralunipunjab.com/Teaching/Final%20Details-t10-2013.pdf, http://www.centralunipunjab.com/Teaching/Advertisement-t10-2013.jpg

Last Apply Date: 31 Dec 2014

]]> https://bioinformaticsonline.com/pages/view/34463/single-cell-rnaseq-data-analysis-tutorial Mon, 27 Nov 2017 16:24:29 -0600 https://bioinformaticsonline.com/pages/view/34463/single-cell-rnaseq-data-analysis-tutorial <![CDATA[Single Cell RNAseq data analysis tutorial !!]]>
  • A major breakthrough (replaced microarrays) in the late 00’s and has been widely used since
  • Measures the average expression level for each gene across a large population of input cells
  • Useful for comparative transcriptomics, e.g. samples of the same tissue from different species
  • Useful for quantifying expression signatures from ensembles, e.g. in disease studies
  • Insufficient for studying heterogeneous systems, e.g. early development studies, complex tissues (brain)
  • Does not provide insights into the stochastic nature of gene expression

    • Following are the useful links:

    Single Cell RNAseq data analysis Tutorial

    A step-by-step workflow for low-level analysis of single-cell RNA-seq data

    A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor

    SCell: single-cell RNA-seq analysis software

    https://github.com/diazlab/SCell

    Beta-Poisson model for single-cell RNA-seq data analyses

    https://github.com/nghiavtr/BPSC

    Sincera: A Computational Pipeline for Single Cell RNA-Seq Profiling Analysis

    https://research.cchmc.org/pbge/sincera.html

    SC3 – consensus clustering of single-cell RNA-Seq data

    http://biorxiv.org/content/early/2016/09/02/036558

    Citrus: A toolkit for single cell sequencing analysis

    http://biorxiv.org/content/early/2016/09/14/045070

    Single-Cell Resolution of Temporal Gene Expression during Heart Development

    http://www.cell.com/developmental-cell/fulltext/S1534-5807(16)30682-7

    Scalable latent-factor models applied to single-cell RNA-seq data separate biological drivers from confounding effects

    http://biorxiv.org/content/early/2016/11/15/087775

    Single cell transcriptomes identify human islet cell signatures and reveal cell-type-specific expression changes in type 2 diabetes

    http://genome.cshlp.org/content/early/2016/11/18/gr.212720.116.abstract

    SCODE: An efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation

    http://biorxiv.org/content/early/2016/11/21/088856

    SCOUP is a probabilistic model to analyze single-cell expression data during differentiation

    https://github.com/hmatsu1226/SCOUP

    scLVM is a modelling framework for single-cell RNA-seq data

    https://github.com/PMBio/scLVM

    Selective Locally linear Inference of Cellular Expression Relationships (SLICER) algorithm for inferring cell trajectories

    https://github.com/jw156605/SLICER

    SinQC: A Method and Tool to Control Single-cell RNA-seq Data Quality

    http://www.morgridge.net/SinQC.html

    TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis

    https://github.com/zji90/TSCAN

    Visualization and cellular hierarchy inference of single-cell data using SPADE

    http://www.nature.com/nprot/journal/v11/n7/full/nprot.2016.066.html

    OEFinder: Identify ordering effect genes in single cell RNA-seq data

    https://github.com/lengning/OEFinder

    ]]>     Robert M Willioms     https://bioinformaticsonline.com/bookmarks/view/43631/pangolin-tutorial Fri, 10 Dec 2021 05:58:59 -0600 https://bioinformaticsonline.com/bookmarks/view/43631/pangolin-tutorial <![CDATA[Pangolin tutorial !]]> This is a tutorial for using the Pangolin Web Application. For information on using the command line tool, please visit the command line tool usage page.

    https://cov-lineages.org/resources/pangolin/tutorial.html

    Address of the bookmark: https://cov-lineages.org/resources/pangolin/tutorial.html

    ]]>     Abhi     https://bioinformaticsonline.com/researchlabs/view/12995/national-center-for-bioinformatics-ncb Wed, 23 Jul 2014 14:10:49 -0500 <![CDATA[National Center for Bioinformatics (NCB)]]> NCB is offering M.Phil and Ph.D programs in the area of Bioinformatics. The major goal of NCB is to promote quality training and research in the area of Bioinformatics. Bioinformatics originated as a cross-disciplinary field as the need for computational sections to research problem raised in biomedicine.

    More at http://ncb.qau.edu.pk/

    ]]>