2014 09-29 2nd monday overview
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This document provides an overview of genomics and key concepts in bioinformatics. It discusses how genomics uses DNA sequencing and bioinformatics to analyze genomes. Several challenges and techniques in bioinformatics are then outlined, including using Unix and high performance computing, algorithms for sequence alignment, biological databases, and genome assembly and variant calling.
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swarm optimization, etc. However, with the advancement in wireless communications, more and
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Similar to 2014 09-29 2nd monday overview (20)
CCC-Bicluster Analysis for Time Series Gene Expression Data
CCC-Bicluster Analysis for Time Series Gene Expression Data
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Survey on chromosome image analysis for abnormality detection in leukemias
Comparative analysis of dynamic programming algorithms to find similarity in ...
Comparative analysis of dynamic programming algorithms to find similarity in ...
A clonal based algorithm for the reconstruction of genetic network using s sy...
A clonal based algorithm for the reconstruction of genetic network using s sy...
A clonal based algorithm for the reconstruction of
A clonal based algorithm for the reconstruction of
APPLICATION OF GENETIC ALGORITHM IN DESIGNING A SECURITY MODEL FOR MOBILE ADH...
APPLICATION OF GENETIC ALGORITHM IN DESIGNING A SECURITY MODEL FOR MOBILE ADH...
Intelligent Controller Design for a Chemical Process
Intelligent Controller Design for a Chemical Process
IRJET- Classification of Crops and Analyzing the Acreages of the Field
IRJET- Classification of Crops and Analyzing the Acreages of the Field
More from Yannick Wurm
2018 09-03-ses open-fair_practices_in_evolutionary_genomics
This document discusses the experience of a researcher in genomics with applying FAIR and open approaches. It notes that making data and analysis methods FAIR and open can increase visibility, drive citations, and facilitate collaboration. However, it also enables competition to more easily access and utilize resources without contributing. Striking the right balance between openness and protecting competitive advantages is challenging. Overall, the researcher finds FAIR and open principles have greatly increased the impact and robustness of their work, but there are also costs to consider.
2018 08-reduce risks of genomics research
Geoffrey Chang, a protein crystallographer at The Scripps Research Institute, had his career trajectory disrupted when several of his high-profile papers describing protein structures had to be retracted. An in-house software program Chang's lab used to process diffraction data from protein crystals introduced a sign error that inverted the structures, invalidating biological interpretations. This included a 2001 Science paper describing the structure of the MsbA protein. A 2006 Nature paper by Swiss researchers casting doubt on Chang's MsbA structure led him to discover the software error. Chang and his co-authors sincerely regretted the confusion and unproductive research caused by the need to retract their influential papers.
2017 11-15-reproducible research
Geoffrey Chang was a prominent structural biologist who received prestigious early career awards. However, his work came under scrutiny when other researchers discovered errors in his published protein structures due to a problem with his in-house data analysis software. This led Chang to retract 5 of his papers describing protein structures. The retractions were costly for Chang's career and reputation as well as for other researchers who had performed follow-up work based on the incorrect structures. The incident highlights the importance of using well-tested, reproducible analysis methods in scientific research.
2016 09-16-fairdom
Keynote talk given at Fairdom User meeting http://fair-dom.org/communities/users/barcelona-2016-first-user-meeting/ .
I begin by summarising how we apply molecular approaches to understand social behaviour in ants. Subsequently, I give an overview of the data-handling challenges the genomic bioinformatics community faces. Finally, I give an overview of some of the tools and approaches my lab have developed to help us get things done better, faster, more reliably and more reproducibly.
2016 05-31-wurm-social-chromosome
The document discusses the genetic basis of social organization in fire ant populations. Researchers used RAD sequencing of haploid males to discover SNPs and genotype individuals at over 2,400 loci. Principal component analysis separated individuals into two clusters corresponding to their social form (single or multiple queen), with the first principal component explaining over 12% of the variance. A region on chromosome 13 containing the Gp-9 gene was completely associated with social form. This research identified a major gene influencing an important social trait using next-generation sequencing techniques.
2016 05-30-monday-assembly
This document provides an agenda for a spring school on bioinformatics and population genomics, including practical sessions on analyzing genomic data from reads to reference genomes and gene predictions in 6 steps: inspecting and cleaning reads, genome assembly, assessing assembly quality, predicting protein-coding genes, assessing gene prediction quality, and assessing the overall process quality using biological measures. It also addresses wifi issues that could reduce bandwidth and lists the VM password.
2016 05-29-intro-sib-springschool-leuker bad
This document provides information about a spring school on bioinformatics and population genomics that includes practical sessions. The sessions will cover topics like short read cleaning, genome assembly, gene prediction, quality control, mapping reads to call variants, visualizing variants, analyzing variants through PCA and measuring diversity and differentiation, inferring population sizes and gene flow, and analyzing gene expression from raw sequencing data to expression levels. The document lists the team of practitioners leading the sessions and encourages participants to share their favorite software packages.
2015 12-18- Avoid having to retract your genomics analysis - Popgroup Reprodu...
Brief (15min) talk I gave at #PopGroup49 in Edinburgh providing a few simple methods to reduce risk in genomics analyses.
Please cite: Avoid having to retract your genomics analysis (2015) Y Wurm. The Winnower 2, e143696.68941 https://thewinnower.com/papers/avoid-having-to-retract-your-genomics-analysis
2015 11-17-programming inr.key
This document contains information about programming in R, including practical examples. It discusses accessing and subsetting data, using regular expressions for text search, creating functions, and using loops. Examples are provided to demonstrate creating vectors, accessing subsets of vectors, using regular expressions to find patterns in text, creating functions to convert between units or estimate values, and using for loops to repeat operations over multiple elements. The document suggests R is useful for working with big data in biology and other fields due to its ability to automate tasks, integrate with other tools, and handle large datasets through programming.
2015 11-10-bio-in-docker-oswitch
This document describes oSwitch, a tool that allows easy access to other operating systems via one-line commands. It works by wrapping Docker containers, allowing commands to be run in different OS environments without disrupting the user's current environment. The document provides an example usage where a user is able to run an "abyss-pe" command in a Biolinux container after it is not found in their native OS. It notes how oSwitch aims to preserve the user's current working directory, login shell, home directory and file permissions during usage.
Week 5 genetic basis of evolution
This document provides an outline for a lecture on the genetic basis of evolution. It begins with introducing key terms like gene, locus, allele, genotype, and phenotype. It then discusses genetic drift and how drift is influenced by population size. Selection is also introduced and defined as a process where individuals with different genotypes have different fitnesses. The document emphasizes that both genetic drift and selection influence evolution, and neither process should be overemphasized. It aims to move people away from only considering selection (pan-selectionism) and highlights the importance of genetic drift.
Biol113 week4 evolution
This document discusses human evolution and recent insights from genomics. It summarizes that Neanderthals were the closest evolutionary relatives to modern humans and lived in Europe and Western Asia until disappearing 30,000 years ago. A draft sequence of the Neanderthal genome from three individuals was presented, composed of over 4 billion nucleotides. Comparisons with five modern human genomes identified regions potentially affected by selection in ancestral modern humans, involving genes related to metabolism, cognition, and skeletal development. Analysis suggests Neanderthals shared more genetic variants with non-Africans, indicating gene flow from Neanderthals into their ancestors occurred before Eurasian groups diverged.
Evolution week3
The document discusses analyzing ancient plant and insect DNA extracted from ice core samples in Greenland. Key points:
- Plant and insect DNA was recovered from silty ice samples taken between 2-3 km deep in the Dye 3 and JEG ice cores in Greenland, dating back to before the last glacial period.
- The DNA was identified as coming from tree species like pine and alder, indicating a boreal forest environment in southern Greenland at the time, rather than today's Arctic conditions.
- Other plant species identified include those from orders like Asterales, Poales, Rosales and Malpighiales. Insect DNA from Lepidoptera was also recovered.
2015 10-7-11am-reproducible research
1. The document discusses best practices for scientific software development, including writing code for people rather than computers, automating repetitive tasks, using version control, and conducting code reviews.
2. Specific approaches and tools recommended are planning for mistakes, automated testing, continuous integration, and using a coding style guide. R and Ruby style guides are provided as examples.
3. The benefits of following such practices are improving productivity, reducing errors, making code easier to read and maintain, and allowing scientists to focus on scientific questions rather than software issues. Reproducible and sustainable software is the overall goal.
2015 10-7-9am regex-functions-loops.key
This document provides an introduction to regular expressions (regex) for text search and pattern matching. It explains that regex allows for powerful text searches beyond simple keywords. Various special symbols and constructs are demonstrated that allow matching complex patterns and variants in text. Examples show matching names, sequences, microsatellite repeats and more with regex. Functions, loops and logical operators in R programming are also briefly covered.
Evolution week2
The document discusses major geological drivers of evolution including tectonic plate movement, vulcanism, climate change, and meteorite impacts. Tectonic plate movement has caused continental drift and formation of supercontinents like Pangaea, affecting species distributions. Vulcanism causes both local and global climate changes through emission of gases and particles and formation of new land barriers and islands. Climate changes over geological timescales have also impacted evolution. Meteorite impacts have precipitated mass extinctions. These geological forces alter Earth's conditions and drive evolution through large-scale migrations, speciation events, mass extinctions, and adaptive radiations.
2015 9-30-sbc361-research methcomm
This document provides an overview and schedule for the course "SBC 361 Research Methods & Comms". The course is a mixture of advanced analytical skills taught in computer labs using the programming language R, and theoretical content covered in lectures and workshops. It includes two workshops on careers in science and popular science writing. Students will complete assignments involving the computer practicals and tutorials, and a mock exam. The schedule details the topics to be covered each week by different professors and teaching staff. It emphasizes the importance of attending classes, completing required work, and doing additional outside reading to succeed in the course.
2015 09-29-sbc322-methods.key
This document discusses computational methods and challenges for genome assembly using next-generation sequencing data. It describes the four main stages of genome assembly as preprocessing filtering, graph construction, graph simplification, and postprocessing filtering. Each stage processes the data from the previous stage to build the assembly graph and reduce complexity, though some assemblers delay filtering steps.
Sbc322 intro.key
This document outlines the course SBC322 Ecological and Evolutionary Genomics. It discusses how new genomic technologies have changed ecology and evolution research by merging molecular and ecological approaches. It aims to critically evaluate research questions, methods, experimental designs and applications in ecological and evolutionary genomics. The course will improve students' skills in critically reading literature, understanding interdisciplinary science, and oral and written scientific communication through interactive small group work, informal and formal presentations, blog posts, and peer review.
2015 09-28 bio721 intro
The document provides an overview of topics covered in a bioinformatics course, including using Unix, bioinformatics algorithms, biological databases, sequencing technologies, and genome assembly and variant identification. It lists challenges for students in each topic area and provides examples of concepts that will be covered, such as using HPC systems, dynamic programming for sequence alignment, accessing databases like NCBI, processing sequencing data, and identifying variants from assembly. Images are included of different organisms like ants and sequencing technologies. The document aims to outline the scope and challenges of the bioinformatics course.
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2018 09-03-ses open-fair_practices_in_evolutionary_genomics
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The debris of the ‘last major merger’ is dynamically young
The Milky Way’s (MW) inner stellar halo contains an [Fe/H]-rich component with highly eccentric orbits, often referred to as the
‘last major merger.’ Hypotheses for the origin of this component include Gaia-Sausage/Enceladus (GSE), where the progenitor
collided with the MW proto-disc 8–11 Gyr ago, and the Virgo Radial Merger (VRM), where the progenitor collided with the
MW disc within the last 3 Gyr. These two scenarios make different predictions about observable structure in local phase space,
because the morphology of debris depends on how long it has had to phase mix. The recently identified phase-space folds in Gaia
DR3 have positive caustic velocities, making them fundamentally different than the phase-mixed chevrons found in simulations
at late times. Roughly 20 per cent of the stars in the prograde local stellar halo are associated with the observed caustics. Based
on a simple phase-mixing model, the observed number of caustics are consistent with a merger that occurred 1–2 Gyr ago.
We also compare the observed phase-space distribution to FIRE-2 Latte simulations of GSE-like mergers, using a quantitative
measurement of phase mixing (2D causticality). The observed local phase-space distribution best matches the simulated data
1–2 Gyr after collision, and certainly not later than 3 Gyr. This is further evidence that the progenitor of the ‘last major merger’
did not collide with the MW proto-disc at early times, as is thought for the GSE, but instead collided with the MW disc within
the last few Gyr, consistent with the body of work surrounding the VRM.
Travis Hills' Endeavors in Minnesota: Fostering Environmental and Economic Pr...
Travis Hills of Minnesota developed a method to convert waste into high-value dry fertilizer, significantly enriching soil quality. By providing farmers with a valuable resource derived from waste, Travis Hills helps enhance farm profitability while promoting environmental stewardship. Travis Hills' sustainable practices lead to cost savings and increased revenue for farmers by improving resource efficiency and reducing waste.
Cytokines and their role in immune regulation.pptx
This presentation covers the content and information on "Cytokines " and their role in immune regulation .
Deep Software Variability and Frictionless Reproducibility
Deep Software Variability and Frictionless ReproducibilityUniversity of Rennes, INSA Rennes, Inria/IRISA, CNRS
The ability to recreate computational results with minimal effort and actionable metrics provides a solid foundation for scientific research and software development. When people can replicate an analysis at the touch of a button using open-source software, open data, and methods to assess and compare proposals, it significantly eases verification of results, engagement with a diverse range of contributors, and progress. However, we have yet to fully achieve this; there are still many sociotechnical frictions.
Inspired by David Donoho's vision, this talk aims to revisit the three crucial pillars of frictionless reproducibility (data sharing, code sharing, and competitive challenges) with the perspective of deep software variability.
Our observation is that multiple layers — hardware, operating systems, third-party libraries, software versions, input data, compile-time options, and parameters — are subject to variability that exacerbates frictions but is also essential for achieving robust, generalizable results and fostering innovation. I will first review the literature, providing evidence of how the complex variability interactions across these layers affect qualitative and quantitative software properties, thereby complicating the reproduction and replication of scientific studies in various fields.
I will then present some software engineering and AI techniques that can support the strategic exploration of variability spaces. These include the use of abstractions and models (e.g., feature models), sampling strategies (e.g., uniform, random), cost-effective measurements (e.g., incremental build of software configurations), and dimensionality reduction methods (e.g., transfer learning, feature selection, software debloating).
I will finally argue that deep variability is both the problem and solution of frictionless reproducibility, calling the software science community to develop new methods and tools to manage variability and foster reproducibility in software systems.
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The use of Nauplii and metanauplii artemia in aquaculture (brine shrimp).pptx
Although Artemia has been known to man for centuries, its use as a food for the culture of larval organisms apparently began only in the 1930s, when several investigators found that it made an excellent food for newly hatched fish larvae (Litvinenko et al., 2023). As aquaculture developed in the 1960s and ‘70s, the use of Artemia also became more widespread, due both to its convenience and to its nutritional value for larval organisms (Arenas-Pardo et al., 2024). The fact that Artemia dormant cysts can be stored for long periods in cans, and then used as an off-the-shelf food requiring only 24 h of incubation makes them the most convenient, least labor-intensive, live food available for aquaculture (Sorgeloos & Roubach, 2021). The nutritional value of Artemia, especially for marine organisms, is not constant, but varies both geographically and temporally. During the last decade, however, both the causes of Artemia nutritional variability and methods to improve poorquality Artemia have been identified (Loufi et al., 2024).
Brine shrimp (Artemia spp.) are used in marine aquaculture worldwide. Annually, more than 2,000 metric tons of dry cysts are used for cultivation of fish, crustacean, and shellfish larva. Brine shrimp are important to aquaculture because newly hatched brine shrimp nauplii (larvae) provide a food source for many fish fry (Mozanzadeh et al., 2021). Culture and harvesting of brine shrimp eggs represents another aspect of the aquaculture industry. Nauplii and metanauplii of Artemia, commonly known as brine shrimp, play a crucial role in aquaculture due to their nutritional value and suitability as live feed for many aquatic species, particularly in larval stages (Sorgeloos & Roubach, 2021).
What is greenhouse gasses and how many gasses are there to affect the Earth.
What are greenhouse gasses how they affect the earth and its environment what is the future of the environment and earth how the weather and the climate effects.
Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...
Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...University of Maribor
Slides from talk:
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11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Inter-Society Networking Panel GRSS/MTT-S/CIS Panel Session: Promoting Connection and Cooperation
https://www.etran.rs/2024/en/home-english/8.Isolation of pure cultures and preservation of cultures.pdf
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Deep Behavioral Phenotyping in Systems Neuroscience for Functional Atlasing a...
Functional Magnetic Resonance Imaging (fMRI) provides means to characterize brain activations in response to behavior. However, cognitive neuroscience has been limited to group-level effects referring to the performance of specific tasks. To obtain the functional profile of elementary cognitive mechanisms, the combination of brain responses to many tasks is required. Yet, to date, both structural atlases and parcellation-based activations do not fully account for cognitive function and still present several limitations. Further, they do not adapt overall to individual characteristics. In this talk, I will give an account of deep-behavioral phenotyping strategies, namely data-driven methods in large task-fMRI datasets, to optimize functional brain-data collection and improve inference of effects-of-interest related to mental processes. Key to this approach is the employment of fast multi-functional paradigms rich on features that can be well parametrized and, consequently, facilitate the creation of psycho-physiological constructs to be modelled with imaging data. Particular emphasis will be given to music stimuli when studying high-order cognitive mechanisms, due to their ecological nature and quality to enable complex behavior compounded by discrete entities. I will also discuss how deep-behavioral phenotyping and individualized models applied to neuroimaging data can better account for the subject-specific organization of domain-general cognitive systems in the human brain. Finally, the accumulation of functional brain signatures brings the possibility to clarify relationships among tasks and create a univocal link between brain systems and mental functions through: (1) the development of ontologies proposing an organization of cognitive processes; and (2) brain-network taxonomies describing functional specialization. To this end, tools to improve commensurability in cognitive science are necessary, such as public repositories, ontology-based platforms and automated meta-analysis tools. I will thus discuss some brain-atlasing resources currently under development, and their applicability in cognitive as well as clinical neuroscience.
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mô tả các thí nghiệm về đánh giá tác động dòng khí hóa sau đốt
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2014 09-29 2nd monday overview
- 2. Genomics?
- 3. Genomics - Wikipedia Genomics is a discipline in genetics that applies recombinant DNA, DNA sequencing methods, and bioinformatics to sequence, assemble, and analyze the function and structure of genomes (the complete set of DNA within a single cell of an organism).[1][2] Advances in genomics have triggered a revolution in discovery-based research to understand even the most complex biological systems such as brain.[3] The field includes efforts to determine the entire DNA sequence of organisms and fine-scale genetic mapping. The field also includes studies of intragenomic phenomena such as heterosis, epistasis, pleiotropy and other interactions between loci and alleles within the genome.[4] ! ! In contrast, the investigation of the roles and functions of single genes is a primary focus of molecular biology or genetics and is a common topic of modern medical and biological research. Research of single genes does not fall into the definition of genomics unless the aim of this genetic, pathway, and functional information analysis is to elucidate its effect on, place in, and response to the entire genome's networks.[5][6]
- 4. Estevezj - CC3 Wikimedia http://upload.wikimedia.org/wikipedia/commons/7/73/Number_of_prokaryotic_genomes_and_sequencing_costs.svg Ⓐ Ⓑ Ⓒ
- 5. • Genomics • Biodiversity assessments • Stool microbiome sequencing • Personalized medicine • Cancer genomics
- 6. Challenges 1. Getting up and running with Unix 2. Algorithms in Bioinformatics: strengths & weaknesses 3. Bioinformatics databases 4. DIY: genome assembly & identifying variants.
- 7. Getting up and running with Unix & High Performance Computing (HPC) ITS Research Team (Lukasz Zalewski): 1. Install virtualbox & biolinux. 2. Introduction to Unix 3. Using Apocrita HPC = “the cluster” !
- 8. Algorithms for sequence alignment. - dotplots- the concept of distance: Euclidean, hamming, Levenshtein - dynamic programming and the Smith Waterman algorithm - local, global, semiglobal alignments - gap penalty models - basics of approximate methods (Blast) - scoring matrices (PAM, Blosum) - Profiles and PSI-Blast
- 9. Algorithms for sequence alignment. Take home message? •Algorithms are approximate •Results aren’t perfect •Computers can get it wrong
- 10. BLAST is unable to detect any similarity between these 2 sequences: Gp-9 1 ATGAAGACGTTCGTATTGCATATTTTTATTTTTGCTCTCGTGGCTTTCGCTTCTGCATCT 60 ||||||||||| |||||||||| ||||||||| |||||||| |||||||||| ||||| K2000 1 ATGAAGACGTTGGTATTGCATAATTTTATTTT---TCTCGTGGATTTCGCTTCTCCATCT 57 ! Gp-9 61 CGTGATAGCGCGAGGAAGATAGGATCCCAATATGACAATTACGCGACTTGCTTAGCCGAA 120 ||||| ||||||| || ||| ||||||||| |||||| |||||| ||||||||| ||||| K2000 58 CGTGAGAGCGCGAAGACGATGGGATCCCAACATGACATTTACGCCACTTGCTTACCCGAA 117 ! Gp-9 121 CATAGTCTAACAGAGGATGACATCTTCTCGATTGGTGAAGTATCAAGTGGCCAGCACAAA 180 |||| ||||| || |||| || | ||||||||| ||||||||| |||||||||| ||||| K2000 118 CATAATCTAAGAGGGGATAACGTTTTCTCGATTCGTGAAGTATAAAGTGGCCAGGACAAA 177 ! Gp-9 181 ACCAATCATGAAGATACCGAACTACACAAAAATGGTTGCGTCATGCAATGTTTGTTAGAA 240 |||| ||||||||| |||||||| ||||||||| || ||||||| |||||||| |||||| K2000 178 ACCAGTCATGAAGAAACCGAACTCCACAAAAATCGTCGCGTCATACAATGTTTATTAGAA 237 ! Gp-9 241 AAAGATGGACTGATGTCTGGAGCTGATTATGATGAAGAGAAAATGCGTGAGGACTATATC 300 |||||||| |||||| ||| ||| ||||||||| ||| |||||||||| ||||||||| K2000 238 TAAGATGGAATGATGTGTGGGGCTAATTATGATGGAGAAAAAATGCGTGCTGACTATATC 297 ! Gp-9 301 AAGGAA------ACAGGTGCTCAACCAGGAGATCAAAGGATAGAAGCTCTGAATGCCTGC 354 | |||| || |||| |||||||||| |||| |||| |||| |||||||||| | | K2000 298 AGGGAATCAGGTACCGGTGGTCAACCAGGACATCAGAGGAGAGAACCTCTGAATGCGTAC 357 ! Gp-9 355 ATGCAAGAAACAAAAGACATGGAGGATAAATGTGACAAAAGCTTGCTCCTTGTAGCATGT 414 ||||||||| ||||||| ||| ||| |||||| ||||||||| | || ||| ||||| K2000 358 ATGCAAGAATCAAAAGATATGCAGGTTAAATGGCACAAAAGCT---TTCTAGTAACATGT 414 ! Gp-9 415 GTCTTAGCAGCTGAAGCTGTGCTCGCCGATTCTAACGAAGGAGCATAA 462 | |||||||| | |||||| ||||| |||||| ||||||||| |||| K2000 415 ATTTTAGCAGCGGGAGCTGTTCTCGCGGATTCTCACGAAGGAGAATAA 462
- 11. Algorithms for sequence alignment. Take home message? • Algorithms are approximate • Results depend on: • underlying biology • approximations made by algorithms • search and database size
- 12. Databases for Bioinformatics • Biological databases & access to the annotated genomes • NCBI • Ensembl • UCSC • Entrez & Biomart • Genbank/Uniprot ! • Cancer resources and data portals • TCGA, ICGC and Cosmic
- 13. Databases for Bioinformatics Take home message?
- 14. Genome Assembly & variant calling • Processing raw data • Genome assembly algorithms • Read mapping • Quality Assurance processes • Calling & visualising variants • Automated gene prediction • Doing things in the command-line
- 15. Bruno Vieira Rodrigo Pracana
- 16. Old & modern assembly algorithms • Overlap-layout consensus ! • De bruijn-based.