BOL: Related items

iMAGine - in silico MetAGenomics pipeline

BioStar — Sat, 06 Jul 2024 04:32:18 -0500

iMAGine is a metagenomic workflow which includes filtering, assembling, and binning.

This workflow includes the following tools which are needed to be installed in the system.

Address of the bookmark: https://github.com/avishekdutta14/iMAGine

Sequanix: a dynamic graphical interface for Snakemake workflows

BioStar — Wed, 12 Feb 2020 01:20:34 -0600

A Python library dedicated to NGS analysis (e.g., tools to visualise standard NGS formats).
A set of pipelines dedicated to NGS in the form of Snakefiles (Makefile-like with Python syntax based on snakemake framework) with more than 80 re-usable rules (see Rules).
Original tools to help in the creation of such pipelines including HTML reports.
Standalone applications:
1. sequana_coverage ease the extraction of genomic regions of interest and genome coverage information
2. sequana_taxonomy performs a quick taxonomy of your FastQ. This requires dedicated databases to be downloaded.
3. Sequanix: GUI for snakemake workflows, a GUI for Snakemake workflows (hence Sequana pipelines as well)
More at https://sequana.readthedocs.io/en/master/

Address of the bookmark: https://github.com/sequana/sequana

RNA-Seq differential expression work flow using DESeq2

BioStar — Mon, 23 Aug 2021 10:57:14 -0500

One of the aim of RNAseq data analysis is the detection of differentially expressed genes. The package DESeq2 provides methods to test for differential expression analysis.

Address of the bookmark: http://www.sthda.com/english/wiki/rna-seq-differential-expression-work-flow-using-deseq2

scikit-learn

Jitendra Prajapati — Mon, 29 Feb 2016 17:39:24 -0600

Machine Learning in Python

Simple and efficient tools for data mining and data analysis
Accessible to everybody, and reusable in various contexts
Built on NumPy, SciPy, and matplotlib
Open source, commercially usable - BSD license

More at http://scikit-learn.org/stable/index.html

Address of the bookmark: http://scikit-learn.org/stable/auto_examples/index.html

R tuorial

Rahul Nayak — Mon, 31 Jul 2017 08:41:40 -0500

R learning resources

https://flowingdata.com/

Address of the bookmark: https://flowingdata.com/

Introduction to Bioinformatics and Computational Biology

Jit — Mon, 25 Jan 2021 01:32:30 -0600

This is the course material for STAT115/215 BIO/BST282 at Harvard University.

Xiaole Shirley Liu (lead instructor)
Joshua Starmer
Martin Hemberg
Ting Wang
Feng Yue

Ming Tang
Yang Liu
Jack Kang
Scarlett Ge
Jiazhen Rong
Phillip Nicol
Maartin De Vries

We thank many colleagues in the community, who helped Dr. Liu in prepare the STAT115/215 BIO/BST282 course over the years.

Address of the bookmark: https://liulab-dfci.github.io/bioinfo-combio/

Bioinformatics in Africa: Part6 - Sudan

BioStar — Sat, 06 Feb 2021 21:20:59 -0600

Commission for Biotechnology & Genetic Engineering Khartoum: The Commission for Biotechnology and Genetic Engineering was established in 9/2/1993 as research unit. In addition to research activities it acts as focal point for the International Center for Biotechnology and Genetic Engineering. The commission conducts researches in order to play a part in solving economical, environmental, health and nutritional problems using modern research techniques with an emphasis on the applied researches in these areas. The laboratories were well furnished with the essential equipments and the catalyst infrastructure to facilitate emergence of a successful for research. The Commission equipped with a computer center and information to serve as informatics and Digital library.

Research Interest and Activities: 1. Plant Genetic Transformations
2. Molecular Population Genetics 3. Detection of human and Animals diseases 4. Breast Cancerspecific protein marker 5. Phytochemical 6. Genomic map 7. Bioremediation 8. Tissue Culture.

Web site and links: www.geocity.cbge.com

Code Golf

Abhi — Wed, 06 Oct 2021 04:17:29 -0500

Code Golf is a game designed to let you show off your code-fu by solving problems in the least number of characters.

Since this is your first time here, I suggest starting with something simple like Fizz Buzz.

Address of the bookmark: https://code.golf/

Prepare for Coding Interview !

Abhi — Tue, 11 Jan 2022 06:14:41 -0600

This is a comprehensive guide to prepare for your next coding interview. It's great for recent graduates and has questions and practice materials structured from traditional big tech interview formats.

While it does not include the latest developments in programming since 2019, it nails the core fundamentals in a very comprehensive and accessible way!

Credits to Kaiyu Zhang, with additional material in the appendix sourced from Reddit.

People say that interviews at Google will cover as much ground as possible. As a new college graduate, the ground that I must capture are the following. Part of the list is borrowed from a reddit post: https://www. reddit.com/r/cscareerquestions/comments/206ajq/my_onsite_interview_experience_at_google/ #bottom-comments.

1. Data structures

2. Trees and Graph algorithms

3. Dynamic Programming

4. Recursive algorithms

5. Scheduling algorithms (Greedy)

6. Caching 1

7. Sorting

8. Files

9. Computability

10. Bitwise operators

11. System design

Online resources on must-read papers in evolutionary biology

BioStar — Fri, 26 Jul 2024 01:39:14 -0500

Online resources on must-read papers in evolutionary biology, for a literature club.

Below is a summary of all answers that we received.

All the best,

Jana and Xiaoyan

1.       *Nick Barton:*

- The textbook "Evolution" by Nick Barton, with resources for
  exploring the literature: Barton, N. H., Briggs, D. E. G., Eisen, J.
  A., Goldstein, D. B., & Patel, N. H. (2007). Evolution. Cold Spring
  Harbor Laboratory Press.

- Papers from a course named "Classics in Evolutionary Biology":

Evolutionary Synthesis
1. Haldane, J. B. S. 1932. The causes of evolution. Longmans. New York.
   (esp. Ch. IV).
2. Fisher, R. A. 1930. The genetical theory of natural selection. Oxford
   University Press, Oxford. Selected Sections - Fundamental Theorem.

Genetic Variation
1a. Lewontin, R. C., and J. L. Hubby. 1966. A molecular approach to
the study of genic heterozygosity in natural populations. II. Amount
of variation and degree of heterozygosity in natural populations of
Drosophila pseudoobscura. Genetics. 54:595-609.

1b. Sachidandam et al. 2001. A map of human genome sequence variation
containing 1.42 million single nucleotide polymorphisms. 409: 928-33.

2. Wright S., Dobzhansky T., Hovanitz W. 1942 Genetics of natural
populations VII The allelism of lethals in the third chromosome of
Drosophila pseudoobscura. Genetics 27: 363-394.

Recombination and evolution
1. Hill, W. G., and A. Robertson. 1966. The effect of linkage on limits
to artificial selection. Genet. Res. 8:269-294.

2. Maynard Smith and Haigh. 1974. The hitch-hiking effect of a favourable
gene. Genet. Res. 23: 23-35.

Understanding sequence variation
1. Begun D. J., Aquadro C. F., 1992 Levels of naturally occurring DNA
polymorphism correlate with recombination rate in Drosophila melanogaster.
Nature 356: 519-520.

2. Green R. E., Reich D., Pääbo S., 2010 A draft sequence of the
Neandertal genome. Science 328: 710-722.

Quantitative Genetics:  variation in complex traits
1. Galton F., 1877 Typical laws of heredity. Nature 15: 492-495-
512-514- 532-533.

2. Turelli M., 1984 Heritable genetic variation via
mutation-selection balance: Lerch's Zeta meets the abdominal
bristle. Theor. Popul. Biol. 25: 138-193.

Quantitative Genetics:  finding the genes
1. Shrimpton A. E., Robertson A., 1988 The Isolation of polygenic factors
controlling bristle score in Drosophila melanogaster II Distribution of
third chromosome bristle effects within chromosome sections. Genetics
118: 445-459.

2. Boyle E. A., Li Y. I., Pritchard J. K., 2017 An expanded view of
complex traits: from polygenic to omnigenic. Cell 169: 1177-1186.

Neutral Evolution
1. Kimura, M. 1968. Evolutionary rate at the molecular level. Science.
217:624-626.

2a. Kern A. D., Hahn M. W., 2018 The Neutral Theory in Light of Natural
Selection. Molecular Biology and Evolution 110: 21077-6.

2b. Jensen J. D., Payseur B. A., Stephan W., Aquadro C. F., Lynch M.,
Charlesworth D., Charlesworth B., 2018 The importance of the Neutral Theory
in 1968 and 50 years on: a response to Kern and Hahn 2018. Evolution 112:
2109-4.

2c. Ellegren & Galtier. 2016. Determinants of genetic diversity. Nature
Reviews Genetics.

Mutation and Genetic Variability
1. Luria, S. E., and M. Delbrück. 1943. Mutations of Bacteria from Virus
Sensitivity to Virus Resistance. Genetics. 28(6):491-511.

2. Hill, W G. 1982. "Rates of Change in Quantitative Traits From Fixation
of New Mutations." Proceedings of the National Academy of Sciences (U.S.A.)
79: 142-45.

Testing for selection
1. McDonald & Kreitman. 1991. Adaptive protein evolution at the Adh locus
in Drosophila. Nature.

2. Begun, et al. Mol. Biol. Evol. 16, 1816-1819 (1999).

3. Siddiq et al. 2016. Experimental test and refutation of a classic case
of molecular adaptation in Drosophila melanogaster.  Nature Ecology &
Evolution.

The shifting balance
1. Wright, S. 1932. The roles of mutation, inbreeding, crossbreeding and
selection in evolution. Proceedings of the VI International Congress of
Genetics: 1. pp 356-366.

2. Coyne, J.A., N.H. Barton, and M. Turelli. 1997. A critique of Wright's
shifting balance theory of evolution.  Evolution 51: 643-671.

3. Barton. 2016. Sewall Wright on Evolution in Mendelian Populations and
the "Shifting Balance". Genetics.

Evolution of Sex
1.  Muller, H.J. 1964. The relation of recombination to mutational advance.
Mutation Res. 1(1):2-9

2. McDonald et al. 2016. Sex speeds adaptation by altering the dynamics of
molecular evolution. Nature.

Kin Selection, Cooperation, and Conflict
1. Hamilton, W. D. 1964. The genetical evolution of social behaviour I.
Journal of Theoretical Biology. 7:1-52.

2. Trivers, R. L. 1974 Parent-offspring conflict. American Zoologist.
14(1):249-264.

Sexual Selection
1. Zahavi, A. 1975. Mate selection - a selection of a handicap. J. Theor.
Biol. 53:205-214.

2. Kirkpatrick, M., and Ryan, M.J. 1991. The evolution of mating
preferences and the paradox of the lek. Nature. 350:33-38.

Fitness Landscapes
1. Dean, A. 1995. A Molecular Investigation of Genotype by Environment
Interactions. Genetics. 139:19-33.

2. Costanzo et al. 2010. The Genetic Landscape of a Cell. Science.

Speciation
1. Coyne, J. A., and H. A. Orr. 1989. Patterns of speciation in Drosophila.
Evolution. 43:362-381.

2. Corbett-Detig et al. 2013. Genetic incompatibilities are widespread
within species. Nature.

2.       *Marcos Antezana:*

Valen, L. v. 1975. Energy and Evolution. University of Chicago, Department
of Biology.

3.       *Remco Folkertsma:*

1. The work by Hopi Hoekstra on local adaptation and oldfield mice

2. Poelstra, J. W., Vijay, N., Bossu, C. M., Lantz, H., Ryll, B., Müller,
I., ... & Wolf, J. B. (2014). The genomic landscape underlying phenotypic
integrity in the face of gene flow in crows. Science, 344(6190), 1410-1414.

4.       *Joshka Kaufmann and Leslie Turner*

They offer us a link to 'papers every evolutionary biologist should read',
the papers are collected by Leslie Turner.
https://static1.squarespace.com/static/53e8cb7ce4b02c4bc3aeeee4/t/5ab8fcb670a6ad55c67fcdf4/1522072758665/EvoBioClassicsRefList.pdf

5.       *Sarah Stockwell*

Matt Ridley collected classic papers in evolutionary biology and printed
part of these papers in his book Evolution (see Matt Ridley. Evolution
(Univ. of Oxford Press, 2nd edition, 2004))