2014 10-01-assembly summaryvariantsoverview
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This document discusses genome assembly and sequencing. It provides advice on sampling, sequencing approaches, scaffolding, input data quality assurance, trimming, filtering, choosing an assembler, and testing parameters. It notes that there is no single best way and that testing many combinations of software, parameters, and formats is required. Understanding everything is not necessary, and 20% of the effort can yield 80% of the results. It also briefly describes the fire ant Solenopsis invicta and its two social forms.
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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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2015 12-18- Avoid having to retract your genomics analysis - Popgroup Reprodu...
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Recently uploaded
Gadgets for management of stored product pests_Dr.UPR.pdf
Insectsplayamajorroleinthedeteriorationoffoodgrainscausingbothquantitativeandqualitativelosses
Wellprovedthatnogranariescanbefilledwithgrainswithoutinsectsastheharvestedproducecontainegg(or)larvae(or)pupae(or)adultinsectinthembecauseoffieldcarryoverinfestationwhichcannotbeavoidedindevelopingcountrieslikeIndia
Simpletechnologiesfortimelydetectionofinsectsinthestoredproduceandtherebyplantimelycontrolmeasures
Summary Of transcription and Translation.pdf
Hello Everyone Here We are Sharing You with The process of protien Synthesis in very short points you will be Able to understand It Very well
SDSS1335+0728: The awakening of a ∼ 106M⊙ black hole⋆
Context. The early-type galaxy SDSS J133519.91+072807.4 (hereafter SDSS1335+0728), which had exhibited no prior optical variations during the preceding two decades, began showing significant nuclear variability in the Zwicky Transient Facility (ZTF) alert stream from December 2019 (as ZTF19acnskyy). This variability behaviour, coupled with the host-galaxy properties, suggests that SDSS1335+0728 hosts a ∼ 106M⊙ black hole (BH) that is currently in the process of ‘turning on’. Aims. We present a multi-wavelength photometric analysis and spectroscopic follow-up performed with the aim of better understanding the origin of the nuclear variations detected in SDSS1335+0728. Methods. We used archival photometry (from WISE, 2MASS, SDSS, GALEX, eROSITA) and spectroscopic data (from SDSS and LAMOST) to study the state of SDSS1335+0728 prior to December 2019, and new observations from Swift, SOAR/Goodman, VLT/X-shooter, and Keck/LRIS taken after its turn-on to characterise its current state. We analysed the variability of SDSS1335+0728 in the X-ray/UV/optical/mid-infrared range, modelled its spectral energy distribution prior to and after December 2019, and studied the evolution of its UV/optical spectra. Results. From our multi-wavelength photometric analysis, we find that: (a) since 2021, the UV flux (from Swift/UVOT observations) is four times brighter than the flux reported by GALEX in 2004; (b) since June 2022, the mid-infrared flux has risen more than two times, and the W1−W2 WISE colour has become redder; and (c) since February 2024, the source has begun showing X-ray emission. From our spectroscopic follow-up, we see that (i) the narrow emission line ratios are now consistent with a more energetic ionising continuum; (ii) broad emission lines are not detected; and (iii) the [OIII] line increased its flux ∼ 3.6 years after the first ZTF alert, which implies a relatively compact narrow-line-emitting region. Conclusions. We conclude that the variations observed in SDSS1335+0728 could be either explained by a ∼ 106M⊙ AGN that is just turning on or by an exotic tidal disruption event (TDE). If the former is true, SDSS1335+0728 is one of the strongest cases of an AGNobserved in the process of activating. If the latter were found to be the case, it would correspond to the longest and faintest TDE ever observed (or another class of still unknown nuclear transient). Future observations of SDSS1335+0728 are crucial to further understand its behaviour. Key words. galaxies: active– accretion, accretion discs– galaxies: individual: SDSS J133519.91+072807.4
CLASS 12th CHEMISTRY SOLID STATE ppt (Animated)
Description:
Dive into the fascinating realm of solid-state physics with our meticulously crafted online PowerPoint presentation. This immersive educational resource offers a comprehensive exploration of the fundamental concepts, theories, and applications within the realm of solid-state physics.
From crystalline structures to semiconductor devices, this presentation delves into the intricate principles governing the behavior of solids, providing clear explanations and illustrative examples to enhance understanding. Whether you're a student delving into the subject for the first time or a seasoned researcher seeking to deepen your knowledge, our presentation offers valuable insights and in-depth analyses to cater to various levels of expertise.
Key topics covered include:
Crystal Structures: Unravel the mysteries of crystalline arrangements and their significance in determining material properties.
Band Theory: Explore the electronic band structure of solids and understand how it influences their conductive properties.
Semiconductor Physics: Delve into the behavior of semiconductors, including doping, carrier transport, and device applications.
Magnetic Properties: Investigate the magnetic behavior of solids, including ferromagnetism, antiferromagnetism, and ferrimagnetism.
Optical Properties: Examine the interaction of light with solids, including absorption, reflection, and transmission phenomena.
With visually engaging slides, informative content, and interactive elements, our online PowerPoint presentation serves as a valuable resource for students, educators, and enthusiasts alike, facilitating a deeper understanding of the captivating world of solid-state physics. Explore the intricacies of solid-state materials and unlock the secrets behind their remarkable properties with our comprehensive presentation.
JAMES WEBB STUDY THE MASSIVE BLACK HOLE SEEDS
The pathway(s) to seeding the massive black holes (MBHs) that exist at the heart of galaxies in the present and distant Universe remains an unsolved problem. Here we categorise, describe and quantitatively discuss the formation pathways of both light and heavy seeds. We emphasise that the most recent computational models suggest that rather than a bimodal-like mass spectrum between light and heavy seeds with light at one end and heavy at the other that instead a continuum exists. Light seeds being more ubiquitous and the heavier seeds becoming less and less abundant due the rarer environmental conditions required for their formation. We therefore examine the different mechanisms that give rise to different seed mass spectrums. We show how and why the mechanisms that produce the heaviest seeds are also among the rarest events in the Universe and are hence extremely unlikely to be the seeds for the vast majority of the MBH population. We quantify, within the limits of the current large uncertainties in the seeding processes, the expected number densities of the seed mass spectrum. We argue that light seeds must be at least 103 to 105 times more numerous than heavy seeds to explain the MBH population as a whole. Based on our current understanding of the seed population this makes heavy seeds (Mseed > 103 M⊙) a significantly more likely pathway given that heavy seeds have an abundance pattern than is close to and likely in excess of 10−4 compared to light seeds. Finally, we examine the current state-of-the-art in numerical calculations and recent observations and plot a path forward for near-future advances in both domains.
Mechanisms and Applications of Antiviral Neutralizing Antibodies - Creative B...
Neutralizing antibodies, pivotal in immune defense, specifically bind and inhibit viral pathogens, thereby playing a crucial role in protecting against and mitigating infectious diseases. In this slide, we will introduce what antibodies and neutralizing antibodies are, the production and regulation of neutralizing antibodies, their mechanisms of action, classification and applications, as well as the challenges they face.
快速办理(UAM毕业证书)马德里自治大学毕业证学位证一模一样
学校原件一模一样【微信：741003700 】《(UAM毕业证书)马德里自治大学毕业证学位证》【微信：741003700 】学位证，留信认证（真实可查，永久存档）原件一模一样纸张工艺/offer、雅思、外壳等材料/诚信可靠,可直接看成品样本，帮您解决无法毕业带来的各种难题！外壳，原版制作，诚信可靠，可直接看成品样本。行业标杆！精益求精，诚心合作，真诚制作！多年品质 ,按需精细制作，24小时接单,全套进口原装设备。十五年致力于帮助留学生解决难题，包您满意。
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6:个人职称评审加20分
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ESA/ACT Science Coffee: Diego Blas - Gravitational wave detection with orbita...
ESA/ACT Science Coffee: Diego Blas - Gravitational wave detection with orbita...Advanced-Concepts-Team
Presentation in the Science Coffee of the Advanced Concepts Team of the European Space Agency on the 07.06.2024.
Speaker: Diego Blas (IFAE/ICREA)
Title: Gravitational wave detection with orbital motion of Moon and artificial
Abstract:
In this talk I will describe some recent ideas to find gravitational waves from supermassive black holes or of primordial origin by studying their secular effect on the orbital motion of the Moon or satellites that are laser ranged.Randomised Optimisation Algorithms in DAPHNE
Slides from talk:
Aleš Zamuda: Randomised Optimisation Algorithms in DAPHNE .
Austrian-Slovenian HPC Meeting 2024 – ASHPC24, Seeblickhotel Grundlsee in Austria, 10–13 June 2024
https://ashpc.eu/
HUMAN EYE By-R.M Class 10 phy best digital notes.pdf
Class 10 human eye notes physics
Handwritten best quality
Methods of grain storage Structures in India.pdf
•Post-harvestlossesaccountforabout10%oftotalfoodgrainsduetounscientificstorage,insects,rodents,micro-organismsetc.,
•Totalfoodgrainproductioninindiais311milliontonnesandstorageis145mt.InIndia,annualstoragelosseshavebeenestimated14mtworthofRs.7,000croreinwhichinsectsaloneaccountfornearlyRs.1,300crores.
•InIndiaoutofthetotalproduction,about30%ismarketablesurplus
•Remaining70%isretainedandstoredbyfarmersforconsumption,seed,feed.Hence,growerneedstoragefacilitytoholdaportionofproducetosellwhenthemarketingpriceisfavourable
•TradersandCo-operativesatmarketcentresneedstoragestructurestoholdgrainswhenthetransportfacilityisinadequate
TOPIC OF DISCUSSION: CENTRIFUGATION SLIDESHARE.pptx
Centrifugation is a powerful technique used in laboratories to separate components of a heterogeneous mixture based on their density. This process utilizes centrifugal force to rapidly spin samples, causing denser particles to migrate outward more quickly than lighter ones. As a result, distinct layers form within the sample tube, allowing for easy isolation and purification of target substances.
Immersive Learning That Works: Research Grounding and Paths Forward
We will metaverse into the essence of immersive learning, into its three dimensions and conceptual models. This approach encompasses elements from teaching methodologies to social involvement, through organizational concerns and technologies. Challenging the perception of learning as knowledge transfer, we introduce a 'Uses, Practices & Strategies' model operationalized by the 'Immersive Learning Brain' and ‘Immersion Cube’ frameworks. This approach offers a comprehensive guide through the intricacies of immersive educational experiences and spotlighting research frontiers, along the immersion dimensions of system, narrative, and agency. Our discourse extends to stakeholders beyond the academic sphere, addressing the interests of technologists, instructional designers, and policymakers. We span various contexts, from formal education to organizational transformation to the new horizon of an AI-pervasive society. This keynote aims to unite the iLRN community in a collaborative journey towards a future where immersive learning research and practice coalesce, paving the way for innovative educational research and practice landscapes.
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Gadgets for management of stored product pests_Dr.UPR.pdf
Gadgets for management of stored product pests_Dr.UPR.pdf
Clinical periodontology and implant dentistry 2003.pdf
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SDSS1335+0728: The awakening of a ∼ 106M⊙ black hole⋆
SDSS1335+0728: The awakening of a ∼ 106M⊙ black hole⋆
Mechanisms and Applications of Antiviral Neutralizing Antibodies - Creative B...
Mechanisms and Applications of Antiviral Neutralizing Antibodies - Creative B...
Microbiology of Central Nervous System INFECTIONS.pdf
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Introduction_Ch_01_Biotech Biotechnology course .pptx
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HUMAN EYE By-R.M Class 10 phy best digital notes.pdf
HUMAN EYE By-R.M Class 10 phy best digital notes.pdf
TOPIC OF DISCUSSION: CENTRIFUGATION SLIDESHARE.pptx
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2014 10-01-assembly summaryvariantsoverview
- 3. Congrats! • first ever genome assembly • complete approach • with real-world cutting edge tools • Some shortcuts: • we used 2% of a eukaryotic (ant) genome • only 1 type of paired reads • only used “one-step” software.
- 4. So you want to do sequence a genome… • Sampling? • algorithms prefer low diversity • Sequencing approach? • paired end? • which sequencer? • what is needed for scaffolding?
- 5. Scaffolding
- 6. So you want to do sequence a genome… • Sampling? • algorithms prefer low diversity • Sequencing approach? • paired end? • which sequencer? • what is needed for scaffolding? • input data Q/A? • sequencer statistics fastqc Unable to detect all errors! • • bio-relevant measurements? (e.g. % mapping to known data)
- 7. So you want to do sequence a genome… • trimming/deduplicating/filtering • removing excess/redundant data • removing errors •Which assembler? • used by others? (publications/ online list/ forum/ assemblathon) • something new? ! • assembly result QA • sequence statistics (e.g., QUAST) • bio-relevant measures (e.g. ,CEGMA)
- 8. Perfect parameters • Instead: need to test many combinations • of trimming • of filtering • different assembly software
- 9. Take home messages • No “best way” • Need to install a lot of software • A lot of work in UNIX - to launch software, to convert formats… • Need to test many parameters • Be careful with qualities!
- 10. No need to understand everything! 20% effort for 80% result
- 11. Calling variants
- 13. Downloaded from www.sciencemag.org on March 12, 2013 Solenopsis invicta fire ants are REPORTS a big problem! very well studied! Ascunce et al 2011
- 14. Solenopsis invicta fire ant: two social forms Single-queen form: Multiple-queen form: ! •1 large queen •Independent founding •Highly territorial •Many sizes of workers ! •2-100 smaller queens •Dependent founding •No inter-colony aggression •All workers similar size