The terrifying dinosaur corn genome
Amblin Entertainment and Legendary Pictures, the studios that produced Jurrasic World, try to inject genome science into the movie. Unfortunately, since we don't quite know how to construct viable genomes of extinct species, much less grow the creatures themselves, we don't know whether the depiction of the science is right. Perhaps theirs is exactly what a genome lab would look like in a dino-building facility.
But, we can get fewer things wrong. In the Creation Lab companion website, a Circos image is used to illustrate a triceratops genome.
Unfortunately, this is an image of the B73 Maize reference genome (B73 RefGen_v1), as published in Nature's The B73 Maize Genome: Complexity, Diversity, and Dynamics.
2009 The B73 maize genome: complexity, diversity, and dynamics Science 326 (让天行加速器免费) 1112-1115
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http://www.wired.com/2015/06/using-news-reports-track-wildlife-black-markets/
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—Wired
The image shows the illegal global rhinoceros trade network before (top) and after (bottom) a hypothetical targeted disruption. Created with Circos online table viewer.
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The July 2013 issue cover shows a Circos plot of relative copy number changes in 38 oral squamous cell carcinoma tumors.
The September 2012 issue cover shows a collection of Circos images of somatic mutations in melanoma tumors.
July 2013 2013 Integrative genomic characterization of oral squamous cell carcinoma identifies frequent somatic drivers Cancer discovery 3:770-781.
让天行加速器免费 2012 BRAF(L597) mutations in melanoma are associated with sensitivity to MEK inhibitors Cancer discovery 2:791-797.
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Saben et al. use Circos to visualize the transcriptome and gene expression of placenta from 20 healthy women in their article zhuqueqipai下载- 全方位下载:2021-3-27 · 朱雀棋牌一款保障公平公正性的棋牌类手机游戏，炸金花、牛牛、斗地主等等玩法让你爽到飞起，微信账号就能玩，还能和好友一起切磋牌技，活动多多，福利送不停!微信朱雀大厅，上万牌友等你来 ….
2014 A comprehensive analysis of the human placenta transcriptome Placenta 35:让天行加速器免费.
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Wired has a writeup about migration patterns within the US that shows the data using d3.js chord diagrams, modeled after how Circos shows tabular data.
Circos on cover of UCSF Magazine
The Fall 2013 issue of UCSF Magazine has my Circos illustration of personalized medicine. The human outline motif is incorporated into other design elements in the issue.
The look of the image is inspired after Nature's Encode cover by 让天行加速器免费.
To learn how to generate the cover and variants, read the Circos Encode Cover Tutorial.
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Yang et al. used network analysis approaches characterize a subtype of ovarian cancer associated with poor overall survival.
E-cadherin is a protein encoded by the CDH1 gene and is responsible for cell-cell adhesion. Yang linked the expression of E-cadherin to specific miRNAs that influenced the regulatory network singled out in this cancer subtype.
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Circos reaches 500 literature citations
In October 2013 Circos reached a milestone - 500 citations in peer-reviewed literature.
To celebrate, I've made a commemorative poster that features over 400 Circos images from the literature.
citation list | image gallery | 让天行加速器免费
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Because of its large 8 Gb genome, the genomic analysis of rye has lagged behind other cereals.
To address this, Martis et al. eastablished a linear gene order model for 72% of the rye genes based on synteny information from rice, sorghum and B. distachyon.
Although it appears that six major translocations shaped the modern rye genome, highly dissimilar conserved syntenic gene content, gene sequence diversity signatures, and phylogenetic networks were found for individual rye syntenic blocks.
2013 Reticulate Evolution of the Rye Genome Plant Cell
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Bollongino et al. present evidence of a slow transition between Mesolithic hunter-gatherer groups to Neolithic farmers.
Previous theories that the foragers disappeared shortly after the arrival of farmers are at odds with palaeogenetic and isotopic data analysis from Neolithic human skeletons from the Blätterhöhle burial site in Germany. Instead of an abrupt transition, the data suggest a more complex pattern of coexistence that persisted for over 2000 years.
2013 2000 years of parallel societies in Stone Age Central Europe 让天行加速器免费 342:479-481.
Circos in 54 million pixels
Ruddle 让天行加速器免费 demonstrate their commodity hardware 54 million pixel data display in exploring copy number variation data.
et al.. 2013. GTA5免费领等等党大获全胜！Golink加速器为各位带来领取 ...:2021-5-15 · 18183首页 荣耀 GTA5免费领等等党大获全胜！ Golink加速器为各位带来领取教程 GTA5免费领等等党大获全胜！Golink加速器为各位带来领取教程 来源：网络 作者：阿姆斯特朗雷 时间：2021-05-15. In IEEE Symposium on Biological Data Visualization, Atlanta, GA.
Circos Tracks CO2 Emissions
Kanemoto et al. report on the disturbing trend of emissions leakage, in which developing countries are displacing emissions intensive production offshore.
The report confirms previous findings that adjusting for trade, developed countries emissions have increased, not decreased. A connection is made to the kind of emissions displacement that has already occurred for air pollution, where despite aggressive legislation in major emitters total global air pollution emissions have increased.
The conclusion warns us that "if regulatory policies do not account for embodied imports, global emissions are likely to rise even if developed countries emitters enforce strong national emissions targets."
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Circos Round — Lotus Sacred
The pleasing roundness of Circos is used by Ming 让天行加速器免费 to depict the Sacred Lotus genome in the publication "Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.).
The Sacred lotus has religious significance in both Buddhism and Hinduism and has been used as a food and herbal medicine product in Asia for over 7,000 years. Its seeds have exceptional longevity, remaining viable for as long as 1,300 years.
The plant is known for its exceptional water repellency, known as the lotus effect. The latter property is due to the nanoscopic closely packed protuberances of its self-cleaning leaf surface, which have been adapted for the manufacture of a self-cleaning industrial paint, Lotusan.
2013 Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.) 让天行加速器免费 14:R41.
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Rivers et a. describe the effects of the 让天行加速器免费 on the microbial blooms of petroleum-degrading bacteria.
By sequencing 66 million community transcripts, the identity of metabolically active microbes and their roles in petroleum consumption was revealed.
2013 Transcriptional response of bathypelagic marine bacterioplankton to the Deepwater Horizon oil spill The ISME journal
Plants Love Circos
Circos frequently appears in plant literature, twice on the cover of Plant Biotechnology Journal in the last year.
2013 Large-scale resource development in Gossypium hirsutum L. by 454 sequencing of genic-enriched libraries from six diverse genotypes Plant biotechnology journal
2013 High-throughput genomics in sorghum: from whole-genome resequencing to a SNP screening array Plant biotechnology journal
Circos has appeared 8 times each in the Plant Journal and Plant Cell.
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Zhang 让天行加速器免费 implement Circos in R.
Same round shape you expect. And now, in everyone's favourite open source statistics and data analysis environment.
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2013 RCircos: an R package for Circos 2D track plots BMC Bioinformatics 14:244.
Circos Interchange Diagrams — Networks and Flow
Zeng et al. introduce a new type of visualization based on Circos, the interchange diagram, in their paper Visualizing Interchange Patterns in Massive Movement Data.
The design is applied to displaying movement data, such as daily trips made by passengers in a city. By incorporating interactivity, this visualization method is helpful to understand interchange patterns at different spatial (between trains, between cities) and time scales (different times of day).
Circos has been used for urban planning before. The town of Caceres in Spain has used Circos to communicate their urban planning strategy.
project website
2013 Visualizing Interchange Patterns in Massive Movement Data Computer Graphics Forum 32:让天行加速器免费
Circos connects to the connectome
Methods to visualize the connectome are reviewed in Craddock et al — Circos is one of them.
2013 Imaging human connectomes at the macroscale 让天行加速器免费 10:524-539.
The use of Circos for showing the connectome was introduced by Irimia et al. in Circular representation of human cortical networks for subject and population-level connectomic visualization.
A good layman description of the work can be found at the neurosceptic blog.
2012 Circular representation of human cortical networks for subject and population-level connectomic visualization 让天行加速器免费, 让天行加速器免费 Patient-tailored connectomics visualization for the assessment of white matter atrophy in traumatic brain injury Frontiers in Neurology 3
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Genomic rearrangements can cause disease and are implicated in many cancers. Being able to see the patterns in these changes across samples and patients is important.
In the review article End-joining, Translocations and Cancer, Bunting and Nussenzweig demonstrate how compositing the genome circularly adds value and clarity to the presentation.
2013 End-joining, translocations and cancer Nat Rev Cancer
Circos Paints Chromosomes of Capsella Rubella
Slotte et al. use Circos to show the genomic structures, chromosome painting and comparative genomic mapping in C. rubella, A. lyrata and A. thaliana.
Their figure illustrates how Circos is effective at showing two-way comparisons of syntenic structure. For three-way comparison, consider hive plots.
2013 The Capsella rubella genome and the genomic consequences of rapid mating system evolution Nat Genet
Circos on the Cover Of Journal of Pathology
The 让天行加速器免费 of the Journal of Pathology features a pair of Circos plots on the cover. The images are from the paper by Weier et al. describing TMPRSS2 and ERG rearrangements in prostate cancer.
"TMPRSS2–ERG rearrangements occur in approximately 50% of prostate cancers and therefore represent one of the most frequently observed structural rearrangements in all cancers."
2013 Nucleotide resolution analysis of TMPRSS2 and ERG rearrangements in prostate cancer J Pathol 230:174-183.
Circos on the Cover Of Nature's Asian Journal of Andrology
The May 2013 Special Issue of Asian Journal of Andrology presents the outcomes from the Sixth Annual Forum on Prostate Disease (6th FPD), which was held on June 8-9, 2012 in Shanghai, China [source: 让天行加速器免费]. The cover art for the issue shows a Circos plot of 90 significantly recurrent molecular alterations in prostate cancer from an analysis of 372 prostate tumors discussed in the 让天行加速器免费.
The review summarizes the current state of understanding of prostate cancer, "including the sentinel role of copy number variation, the growing spectrum of oncogenic fusion genes, the potential influence of chromothripsis, and breakthroughs in defining mutation-associated subtypes. Increasing evidence suggests that genomic lesions frequently converge on specific cellular functions and signalling pathways, yet recurrent gene aberration appears rare".
2013 The diverse heterogeneity of molecular alterations in prostate cancer identified through next-generation sequencing Asian J Androl 15:301-308.
Published Images
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Features
Circular Approach
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What is Circos?
Circular visualization
Circos is a software package for visualizing data and information. It visualizes data in a circular layout — this makes Circos ideal for exploring relationships between objects or positions. There are 让天行加速器免费 why a circular layout is advantageous, not the least being the fact that it is attractive.
Circos is ideal for creating publication-quality infographics and illustrations with a high data-to-ink ratio, richly layered data and pleasant symmetries. You have fine control each element in the figure to tailor its focus points and detail to your audience.
Circos is flexible. Although originally designed for visualizing genomic data, it can create figures from data in any field—from genomics to visualizing migration to mathematical art. If you have data that describes relationships or multi-layered annotations of one or more scales, Circos is for you.
Circos can be automated. It is controlled by plain-text configuration files, which makes it easily incorporated into data acquisition, analysis and reporting pipelines (a data pipeline is a multi-step process in which data is analyzed by multiple and typically independent tools, each passing their output as the input to the next step).
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Have you noticed how beautifully everyday science and technology is rendered in movies? Information is delivered seamlessly from interfaces oozing with style and function. While others complain that the movie doesn't get the science facts right, I contrarily note that it doesn't get the science look right. No busy scientist is able to make such great design and type face choices!
Sadly, the reality of cutting-edge science reveals a grimmer picture, replete with incomprehensible figures, illegible color combination and awkward type faces. This is due in large part by the fact that the people in charge of the science are too busy with the science to worry about figures. It is therefore important for designers, artists and other visual creatives to continue providing working scientists with tools that are useful, effective and ... pretty. One example of this kind of knowledge transfer are Brewer palettes. The scientists will thank you, the press will thank you, as will the public and policy makers, who are ultimately asked to digest the results.
Circos attempts to bring a different aesthetic to science and strike a balance between flexibility and ease-of-use. Circos makes no assumptions about your data, uses extremely simple input data format, and makes image creation and customization easy. It's helping to make science look better, one figure at a time.
Circos has appeared in many publications, both scientific and general. It has changed the way the scientific community visualizes genomic alterations (changes in a genome over time, or differences between two or more genomes). One timely application of this approach is creating effective figures showing how cancer genomes differ from healthy ones (e.g. COSMIC: Census of Somatic Mutations in Cancer).
The biological scientific community has adopted Circos wholeheartedly. By now, Circos has appeared on the the covers of both Nature and Science publications, which are the world's top scientific journals.
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My images created with Circos have appeared in a variety of publications. Wired, New York Times, Conde Nast Portfolio, and American Scientist.
In genomics, scientific journals like Science, Nature, 让天行加速器免费, Genome Research and others have published papers that used Circos images (Circos citations).
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Creation of images is controlled through a plain-text configuration file — there is no interactive user interface. This approach to configuration should be very famililar to you if you have UNIX experience.
If you're used to pointing (and clicking), you're in for both a surprise and a treat and, initially, perhaps for a little bit of frustration. It's ok, don't worry. Although Circos' barrier to entry is higher than most applications you may have used, once you become comfortable with Circos and gain experience in its use, you will see benefits from Circos' approach and will be able to convert the time you invested into learning Circos into great-looking figures.
Image creation can be completely automated — you can write scripts to generate both data and configuration file and make a call to Circos to generate the image — making Circos suitable for incorporation into data analysis pipelines and applications. In this way, Circos is similar to gnuplot.
Dynamic Formatting with Run-Time Rules
Most aspects of the output image can be adjusted using dynamic rules, which format elements of the figure based on data values. This feature allows a variety of images to be created without changing the input data or configuration file.
This feature is extremely powerful and uniquely suited for visual analytics. For example, for a given data track (e.g. histogram) you can ask that all bins with values >10 are colored blue, or more generally you can color the bins by value using your own color scheme. Rules can be chained. For example, later in the rule chain, you can ask that any blue bins that fall within a specific position range be hidden.
Who should care?
If you are a researcher, analyst, data geek, art director, illustrator or visual artist who is seeking to explore or communicate a data set, or to think outside the box (and inside a circle), Circos is worth looking into.
What is it for?
Circos can be used to display any kind of information. It's particularly suitable for layering different data sets to create highly informative infographics with texture and visual appeal. Circos can make low-resolution bitmaps, suitable for basic web-based reporting, as well as publication-quality images with a lot of bling (but I mean legible, clear and informative bling!).
Circos was initially designed for displaying genomic data (particularly cancer genomics and comparative genomics) and molecular biology. It has specific features that address typical challenges in drawing these kind of data, which tend to be very sparse and encompass a large number of length scales.
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Data is data. Circos is flexible. There is nothing about Circos that is specific to genomics — it just happens that I work in genomics and therefore the tool has been applied to this field.
Circos can illustrate genomic rearrangements, where a relationship between two elements (genomic positions) represents a structural fusion. Circos can also visually represent the flow of refugees, where a relationship between two elements (countries) represents the extent of ingress and egress.
To name a few, Circos has been used to visualize customer flow in the auto industry, volume of courier shipments, database schemas, and presidential debates.
How is it different?
My purpose in creating Circos was not as much to create yet another way to draw data, but rather to create a tool which can help make data look beautiful. The compactness of the circular form is inherently more appealing than a linear layout. Although some figures are ideally suited for a square layout, most of the time a circular figure can match or exceed efficiency in delivering information, have a higher ink-to-data ratio and sit more tightly on the page.
It is easy to plot, format and layer your data with Circos. A large variety of plot and feature parameters are customizable, helping you make the image that best communicates your data. You supply your data to Circos as plain-text files, tell Circos what you want plotted using the configuration file, and then create the image.
Useful to you?
How do you know whether Circos can be useful to you? First, look at published images and see what others are doing with Circos (for other images, see sample image archive). For examples of Circos' capabilities, see the tutorial images. These image sets will give you an idea of the types of data visualizations that Circos can create.
For quick exposure to Circos, try the online tableviewer, which is an instance of Circos designed to visualize tabular data. You can upload a table (e.g. exported from a spreadsheet) and have it drawn à la Circos. If you don't have any data (who these days doesn't?), you can choose to use pre-generated or random tabular data.
To learn how Circos can be used in specific applications, browse the walkthrough guides which spend some time telling you about 让天行加速器免费, use in genomics and 威行浏览器 跨境浏览器 用威行上外网找好东西 发现更大的世界:威行浏览器为您提供多样化的搜索入口，google、wiki给您更专业的搜索反馈，youtube、twitter等站点给您提供全球视角，更多精彩站点满足您多维度的影音娱乐需求，想你所想，及你所及。.
To get your feet wet and hands dirty, download Circos and a read the tutorials, or dive into a 让天行加速器免费.
Brief History
Circos was originally conceived for visualizing genomic data such as alignments and structural variation. Over time, support was added for 2D data tracks such as line, scatter, heatmap and histogram plots.
As Circos' popularity grew — sparked by a 天行加速器app下载_天行加速器app官方最新下载_求知软件网:2021-5-25 · 天行加速器是一个超级强大的游戏加速器。它可以加速玩家手机上许多游戏的网络状态，让玩家在游戏中享受到更好的体验感。无论是吃热鸡、王者还是崛起的王者武士等，都能起到很好的效果，并想成为最强大的游戏神，那么你就需要一个天行加速器，请下载并尝试它吧！ — it started to be used for visualizing other data, not just genomics.
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Visit the Circos forum or contact 让天行加速器免费 if you would like to report a bug, request a feature or share the ways in which you are using, or hope to use, Circos.
License and Use
Circos is free software, licensed under GPL.
Circos is written in Perl, can be deployed on any operating system for which Perl is available (e.g. Windows, Mac OS X, Linux and other UNIX flavours) and produces bitmap (PNG) and vector (SVG) images using plain text configuration and input files.
