BOL: Related items

BioCoder : newsletter of that revolution. It’s about biology as it moves from research labs into startup incubators, hacker spaces, and even homes

Jit — Sun, 02 Feb 2020 07:43:52 -0600

BioCoder features:

Novel therapeutic discovery strategies
Hardware such as low-cost lab equipment or diagnostics
Open or low-cost bioinformatics tools
Engineered organisms for the production of small molecules, biologics, or other products
Research projects at a community labspace or projects for science education or public engagement
Hardware or software for lab automation
Citizen science or DIY research projects
Science policy
Tools to increase reproducibility in research, or anything related

Address of the bookmark: https://www.oreilly.com/biocoder/

PhD position in Molecular Cell Biology

Sat, 15 Feb 2020 06:09:55 -0600

https://www.jobvector.de/jobs-stellenangebote/biologie-life-sciences/wissenschaftliche-r-mitarbeiter-in/phd-position-molecular-cell-biology-129604.html?suid=0ec057818886c1eceac674ca3f83943367a6cbe2

Essential experience / qualifications:
We are looking for highly motivated candidates holding a Master / Diploma in Biology, Biochemistry, Molecular Medicine or similar; solid knowledge of molecular and cell biological techniques; good English knowledge.

Applications:
Please send your application (including CV, letter of motivation, contact information of two references, and list of publication) by 13.03.2020 at the latest to:

Universitätsklinikum Erlangen
Chirurgische Klinik
Translational Research Center
Prof. Dr. rer. nat. Michael Stürzl
Schwabachanlage 12
91054 Erlangen
E-Mail: michael.stuerzl@uk-erlangen.de

Bioinformatics Scientist – ICMR Computational Genomics Centre

Sat, 26 Dec 2020 10:18:29 -0600

ICMR invites online applications, from Indian Citizens, up to 8th January 2020 till 5:30 PM to fill up the following post to be filled purely on a temporary basis under “ICMR Computational Genomics Centre” under Dr. Harpreet Singh, Head, Division of Biomedical Informatics (BMI), ICMR HQRS, New Delhi 110029.
The Terms & Conditions for the post are as follows:

a) Scientist-B – UR (2 posts-Bioinformatics) on consolidated salary of Rs.48,000/- pm + HRA

b) Scientist C – UR (1 post -Bioinformatics) on consolidated salary of Rs. 51,000 pm+ HRA

c) Scientist B- UR (2 post-Statistics) on a consolidated salary of Rs.48,000/- pm +HRA

d) Computer Programmer 1 post UR & 1 post SC on a consolidated salary of Rs. 32,500/- pm

e) Research Assistant -UR 1 post on a consolidated salary of Rs. 31,000/- pm

More at https://projectjobs.icmr.org.in/sccbioinformatics/uploads/recruitment/Adv_BMI_24122020.pdf

Computational resources for TE discovery and TE detection

Abhimanyu Singh — Mon, 12 Feb 2018 10:29:18 -0600

Transposable Elements (TEs) to genome structure and evolution as well as their impact on genome sequencing, assembly, annotation and alignment has generated increasing interest in developing new methods for their computational analysis.

Following are the list of resource and location for TE discovery and TE detection:

BLASTER suite http://urgi.versailles.inra.fr/development/blaster/

Censor http://www.girinst.org/censor/download.php

find_ltr http://darwin.informatics.indiana.edu/cgi-bin/evolution/ltr.pl

FINDMITE http://jaketu.biochem.vt.edu/dl_software.htm

HMMER http://hmmer.janelia.org/

LTR_FINDER http://tlife.fudan.edu.cn/ltr_finder/

LTR_STRUC http://www.genetics.uga.edu/retrolab/data/LTR_Struc.html

LTR_MINER http://genomebiology.com/2004/5/10/R79/suppl/s7

LTR_par http://www.eecs.wsu.edu/~ananth/software.htm

MAK http://wesslercluster.plantbio.uga.edu/mak06.html

MaskerAid http://blast.wustl.edu/maskeraid/

mer-engine http://mer-engine.cshl.edu/mer-home.php

mreps http://bioinfo.lifl.fr/mreps/

PILER http://www.drive5.com/piler/

PLOTREP http://repeats.abc.hu/cgi-bin/plotrep.pl

RepBase http://www.girinst.org/

RepeatFinder http://cbcb.umd.edu/software/RepeatFinder/

RepeatGluer http://nbcr.sdsc.edu/euler/intro_tmp.htm

RepeatMasker http://www.repeatmasker.org/

RepeatRunner http://www.yandell-lab.org/repeat_runner/index.html

RepeatScout http://repeatscout.bioprojects.org/

repeat-match http://mummer.sourceforge.net/

REPuter http://www.genomes.de/

RetroMap http://www.burchsite.com/bioi/RetroMapHome.html

SMaRTFinder http://bioinf.dimi.uniud.it/software/software/smartfinder

Tandem Repeats Finder http://tandem.bu.edu/trf/trf.html

Transposon Cluster Finder http://www.mssm.edu/labs/warbup01/paper/files.html

TE nest http://www.plantgdb.org/prj/TE_nest/TE_nest.html

TRANSPO http://alggen.lsi.upc.es/recerca/search/transpo/transpo.html

TSDfinder http://www.ncbi.nlm.nih.gov/CBBresearch/Landsman/TSDfinder/

Tu Lab TE tools http://jaketu.biochem.vt.edu/dl_software.htm

WU-BLAST http://blast.wustl.edu

A computational postdoc position and a bioinformatician position

Thu, 18 Jan 2018 16:29:42 -0600

A computational postdoc position and a bioinformatician position are available in Alessandro Romanel's Lab recently established at the Centre for Integrative Biology (CIBIO) in Trento, Italy. The positions are in the context of an AIRC grant and are immediately available.

Successful candidates will be involved in the design and implementation of strategies to study the role of inherited polymorphisms in combination with timedependent variables and somatic events on cancer genesis, progression and resistance.
The ideal postdoc candidate will have a PhD in Computer Science, Bioinformatics, Computational Biology or equivalent, experience in the analysis of next generation sequencing and high-density array data from human cells, strong analytical and quantitative background and programming skills. Background in cancer genomics is recommended.
The ideal bioinformatician candidate will have a four or five years degree in Computer Science, Bioinformatics or equivalent, experience in the management of large datasets, implementation of processing pipelines and strong programming skills. Background in biology/genomics is a plus.
Highly motivated individuals are invited to send a detailed CV, a cover letter describing research interests and experience, and contact information for two references to Alessandro Romanel (alessandro.romanel@unitn.it).

Nextflow: Data-driven computational pipelines

BioStar — Thu, 20 Feb 2020 00:10:12 -0600

Nextflow enables scalable and reproducible scientific workflows using software containers. It allows the adaptation of pipelines written in the most common scripting languages.

Its fluent DSL simplifies the implementation and the deployment of complex parallel and reactive workflows on clouds and clusters.

More at https://github.com/nextflow-io/nextflow

Address of the bookmark: https://www.nextflow.io/

MetaGraph: Ultra Scalable Framework for DNA Search, Alignment, Assembly

Abhi — Sat, 08 Jun 2024 16:15:25 -0500

The MetaGraph framework is designed to work with a wide range of input data sets, indexing from a few samples up to the contents of entire archives with hundreds of thousands of records. The indexing workflow always follows the same principle, transforming single input samples into error-removed, refined sample graphs, which are then merged into a joint metagraph index. Each input sample is annotated in the joint index as a subgraph. This graph index enriched with metadata can then be used for downstream applications such as sequence search or differential assembly.

Searcg link https://metagraph.ethz.ch/search

Pre-print https://www.biorxiv.org/content/10.1101/2020.10.01.322164v4

Address of the bookmark: https://metagraph.ethz.ch/

repeat-aware: Repeat aware scaffolding evaluation framework by Igor Mandric

Jit — Wed, 21 Mar 2018 18:10:00 -0500

Genome scaffolding is a classical challenging problem in bioinformatics. It refers to joining assembly contigs into chains (called scaffolds). The join between two contigs A and B is considered correct if:

Their relative orientation is correct
Their relative order is correct
The gap estimate is similar to the true distance on the reference

The problem of scaffolding validation is also a challenging one. One of the main issues which hinders from an adequate scaffolding evaluation are genome repeats. The previous standard for evaluation (Hunt et al., Genome Biology, 2014) did not take into account repeats. In this evaluation framework, repeats are taken into account.

The new evaluation framework considers the optimal assignment of contigs in the output scaffolding to contigs in the reference scaffolding in the sense of the number of correct links.

https://github.com/mandricigor/repeat-aware

Address of the bookmark: https://github.com/mandricigor/repeat-aware

ChIPulate: A Python3 framework to simulate read counts in a ChIP-seq experiment

Abhimanyu Singh — Mon, 25 Mar 2019 12:46:47 -0500

ChIP-seq simulation pipeline, ChIPulate, we assess the impact of various biological and experimental sources of variation on several outcomes of a ChIP-seq experiment, viz., the recoverability of the TF binding motif, accuracy of TF-DNA binding detection, the sensitivity of inferred TF-DNA binding strength, and number of replicates needed to confidently infer binding strength.

Address of the bookmark: https://github.com/vishakad/chipulate

Finding a mimicry game for teaching on-line and mentioned general resources

Shruti Paniwala — Tue, 28 Jun 2022 07:32:05 -0500

Mimicry and other resources
Mimicry games:
Great Heliconius game:
http://heliconius.org/evolving_butterflies/
(See also 
https://royalsocietypublishing.org/doi/10.1098/rspb.2020.0014)
Other one, a bit less friendly:
https://ccl.northwestern.edu/netlogo/models/Mimicry
Camouflage practical
https://alexis-catherine.github.io/publication/natural-selection-and-camouflage/
(NetLogo also has one: 
https://ccl.northwestern.edu/netlogo/models/BugHuntCamouflage)
Peppered moth game:
https://askabiologist.asu.edu/peppered-moths-game/play.html

General resources
The always popular Populus:
https://cbs.umn.edu/populus/overview
Drift & Gene Flow 
https://cartwrig.ht/apps/genie/
(Cock van Oosterhout has a great ppt to lead students through this)
See also https://cartwrig.ht/apps/redlynx/
https://demonstrations.wolfram.com/ReplicatorMutatorDynamicsWithThreeStrategies/
NetLogo:
http://ccl.northwestern.edu/netlogo/models/index.cgi
Population Genetics:
https://www.radford.edu/~rsheehy/Gen_flash/popgen/
Evolution in general
https://evolution.berkeley.edu/evolibrary/home.php
Mitochondrial Eve:
https://projects.ncsu.edu/cals/gn/ex/mit-eve.html
Y chromosomes:
https://projects.ncsu.edu/cals/gn/ex/y-chrom.html
A professional online package from Michael Kasumovic:
https://arludo.com/
a compilation of resources:
https://planted.botany.org/index.php?P=Home
Finally, Donald Forsdyke has some great on-line videos explaining
evolutionary principles (occasionally in a fake Scottish accent):
http://post.queensu.ca/~forsdyke/videolectures.htm