The nature of code review

the nature of code review

Thank you for visiting nature. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser or turn off compatibility mode in Internet Explorer. In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript. A Nature Research Journal. Tumour growth is accompanied by tumour evasion of the immune system, a process that is facilitated by immune checkpoint molecules such as programmed cell death protein 1 PD1.

However, the role of tumour glycosylation in immune evasion has mostly been overlooked, despite the fact that aberrant tumour glycosylation alters how the immune system perceives the tumour and can also induce immunosuppressive signalling through glycan-binding receptors.

As such, specific glycan signatures found on tumour cells can be considered as a novel type of immune checkpoint. In parallel, glycosylation of tumour proteins generates neo-antigens that can serve as targets for tumour-specific T cells.

In this Opinion article, we highlight how the tumour 'glyco-code' modifies immunity and suggest that targeting glycans could offer new therapeutic opportunities. Dunn, G.

Cancer immunoediting: from immunosurveillance to tumor escape. McGranahan, N. Clonal heterogeneity and tumor evolution: past, present, and the future. Cell— Blank, C. Science— Chen, D. Oncology meets immunology: the cancer-immunity cycle. Immunity 391—10 Google Scholar.

Sharma, P. The future of immune checkpoint therapy. Science56—61 Varki, A. Glycobiology 21— Protein-glycan interactions in the control of innate and adaptive immune responses. Cagnoni, A.Staff at a car-manufacturing plant in Wuhan, China, observe social-distancing measures during their lunch break.

Less than 36 hours later, he announced on Twitter that he had a fever and a cough. A positive test followed. The disease-tracking scientist had become a data point in his own project.

Ferguson is one of the highest-profile faces in the effort to use mathematical models that predict the spread of the virus — and that show how government actions could alter the course of the outbreak. Research does not get much more policy-relevant than this. The same model suggested that, with no action, the United States might face 2.

the nature of code review

Governments across the world are relying on mathematical projections to help guide decisions in this pandemic. Computer simulations account for only a fraction of the data analyses that modelling teams have performed in the crisis, Ferguson notes, but they are an increasingly important part of policymaking. But, as he and other modellers warn, much information about how SARS-CoV-2 spreads is still unknown and must be estimated or assumed — and that limits the precision of forecasts.

An earlier version of the Imperial model, for instance, estimated that SARS-CoV-2 would be about as severe as influenza in necessitating the hospitalization of those infected. That turned out to be incorrect. The true performance of simulations in this pandemic might become clear only months or years from now. Many of the models simulating how diseases spread are unique to individual academic groups that have been developing them for years.

But the mathematical principles are similar. They are based around trying to understand how people move between three main states, and how quickly: individuals are either susceptible S to the virus; have become infected I ; and then either recover R or die. The R group is presumed to be immune to the virus, so can no longer pass on the infection. People with natural immunity would also belong to this group.

The simplest SIR models make basic assumptions, such as that everyone has the same chance of catching the virus from an infected person because the population is perfectly and evenly mixed, and that people with the disease are all equally infectious until they die or recover. Using detailed information on population size and density, how old people are, transport links, the size of social networks and health-care provision, modellers build a virtual copy of a city, region or an entire country using differential equations to govern the movements and interactions of population groups in space and time.

Then they seed this world with an infection and watch how things unfold. But that, in turn, requires information that can be only loosely estimated at the start of an epidemic, such as the proportion of infected people who die, and the basic reproduction number R 0 — the number of people, on average, to whom one infected person will pass the virus.

The modellers at Imperial, for instance, estimated in their 16 March report 1 that 0. Some parameters, meanwhile, must be entirely assumed.

The Imperial team had to surmise, for instance, that there is no natural immunity to COVID — so the entire population starts out in the susceptible group — and that people who recover from COVID are immune to reinfection in the short term. A simulation run using these parameters would always give the same forecast. But simulations known as stochastic models inject a little randomness — like rolling a virtual dice to see whether or not someone in the I group infects an S person when they meet, for instance.

This gives a range of likely possibilities when the model is run multiple times. But as the groups are broken into smaller, more-representative social subsets to better reflect reality, the models get increasingly complicated. Agent-based models build the same kinds of virtual world as the equation-based ones, but each person can behave differently on a given day or in an identical situation.Welcome to the Nature of Code 2.

In this video, I give an overview of the playlist and The Nature of Code book originally published in Welcome again to Nature of Code!

Code review

Welcome to Nature of Code Chapter 1: Vectors! What is a vector? How do they work in p5. These questions will all be answered in this first section of this series on p5.

This video covers the very basics of vector math focusing on vector addition and looks at how to apply the concept of velocity to a position vector in the random walker example.

In this video, I discuss the difference between static and instance functions in JavaScript and how they are used in the p5. Vector class. This is the foundation on which I will build for implementing forces in the next chapter! In this video, I add a mass property to the Mover class and examine how a mass property impacts gravity and wind forces. In this video, I cover how to read the formula for kinetic friction and incorporate it into a p5. Nature of Code.

1.3: Vector Math - The Nature of Code

These videos accompany The Nature of Code book. This video covers how to initialize a p5 vector with p5.Try being more specific, use different keywords, or checking your spelling we don't judge.

Enrollment for this course has closed. But you can enroll in a future offering please select. Enrollment for this course is currently closed, but the next offering will be available shortly. Check back soon! Can we capture the unpredictable evolutionary and emergent properties of nature in software?

Can understanding the mathematical principles behind our physical world help us to create digital worlds? This class focuses on the programming strategies and techniques behind computer simulations of natural systems. We explore topics ranging from basic mathematics and physics concepts to more advanced simulations of complex systems.

Subjects covered include physics simulation, trigonometry, fractals, cellular automata, self-organization, and genetic algorithms. Examples are demonstrated using the p5. Video featuring original artwork in P5. Verify Your Achievements Whenever you complete a course as a premium member, you can earn a verified Certificate of Accomplishment. These certificates are proof that you completed an online course on our platform.

Easily Shareable Using its unique link, you can share your certificate with everyone from future employers and schools, to friends, family, and colleagues. It's the perfect tool to help you land that new job or promotion, apply to college, or simply share your achievements with the world. Below you will find an overview of the Learning Outcomes you will achieve as you complete this course. While you are completing your Peer Assessments, we ask that you help us maintain the quality of our community.

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It is imperative to know the scope of all these to exercise the power of reviewability against the impugned order of the respective Court. Reference A.

Nature and Scope Section of the Civil Procedure Code empowers a subordinate court to state a case and refer the same for the opinion of the High Court. Such an opinion can be sought when the code itself feels some doubt about a question of Law.

The reference can only be made by a Court but not by a persona designate. A reference can only be made by a Court when there is a reasonable doubt about a question of Law or only when it is of opinion that Act is ultra vires. Unnecessary observations made by the High Court while disposing of the reference having no legal effect must be treated to have been rendered infructuous and superfluous but such power of reference is discretionary.

Object and reference under the proviso.

What is Code Review?

The object for the provision of reference is to enable subordinate courts to obtain in non-appealable cases the opinion of the High Court in the absence of a question of law and thereby avoid the commission of an error which could be remedied later on. When all the following conditions are satisfied the Court is bound to make a reference to the High Court under this proviso under setting out its opinion and the release for it. The right of reference, however, is subject to the conditions prescribed by the order 46 Rule 1 and unless they are fulfilled, the High court cannot entertain a reference form a subordinate Court.

The rule requires the following conditions to be satisfied to enable a subordinate Court to make a reference: i There must be a pending suit or appeal in which the decree is not subject to appeal in which the decree is not subject to appeal or a pending proceeding in execution of such decree; ii A question of law or usage having the force of law must arise in the course of such suit, appeal or proceeding ; and iii The court trying a suit or appeal or executing the decree must entertain doubt on such question.

The question as to the validity of any provision of any Act here a definition in an Act on the ground that it offends Art 14 of the Constitution comes within the proviso to S. Matters within the proviso include the matter of testing the constitutional validity of Any Act, regulation, Ordinance.

Section of the Code and Art of the Constitution. The working of S. The question of the validity of the provision of Act also includes the interpretation of the Constitution when validity is challenged on the grounds that it contravenes an article of the Constitution. The ambit of S. Revision A. Meaning Section of the Code of Civil Procedure empowers A High Court to entertain a revision in any case decided by a subordinate Court in certain circumstances.

This jurisdiction is known as revisional jurisdiction of the High court.Thank you for visiting nature. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser or turn off compatibility mode in Internet Explorer. In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

A Nature Research Journal. Nature Methods is one of several Nature journals undertaking a trial with Code Ocean, a cloud-based reproducibility platform, to make it easier to peer review computational code.

An increasing share of modern research relies on analytical code and software. In turn, a good deal of irreproducible research can be attributed to computational tools that are difficult to decipher, use or recreate. Through the concerted efforts of computational researchers and stricter guidelines from publishers, the culture of scientific software is now more open and geared toward dissemination than ever. Yet, even in the era of Git repositories, peer reviewing code can be frustrating and time consuming.

the nature of code review

Beginning last month, Nature Methodsalong with Nature Biotechnology and Nature Machine Intelligencelaunched a trial with Code Ocean that seeks to facilitate the peer review of computational methods and to improve their reproducibility. Computational tools are complex objects that depend on many components to run. Dependencies include the operating system, programming language, external code libraries, configuration settings and run parameters.

Reproducing these conditions is made even harder by the fact that components typically exist in multiple versions. Many come with their own prerequisites, creating a maddening rabbit hole of dependencies on dependencies. Sincefor papers where custom code is central to the work, Nature Research journals have required that authors include a statement of how their code can be accessed and mention restrictions to access.

More recently, these journals have pledged to take a more active editorial role in encouraging code review. Nature Methods and Nature Biotechnology have a long history of peer reviewing code. In our experience, reviews vary widely in their thoroughness, reflecting a number of factors—reviewer workload and resources, the quality of the code and documentation, and whether the reviewer plans to use the code in his or her own research.

Degree of altruism and caffeine may also be factors. Likewise, numerous problems can surface during the review process. Although this is by no means true for all research software, authors sometimes fail to document all dependencies, and tools can be buggy or can even require software configurations that are not accessible to reviewers.

Code Ocean aims to improve computational reproducibility by offering a web platform that employs Docker technology to execute code in the cloud. Within the platform, it is possible to view or download the code, run routines, and visualize, save or download output, all from a personal computer.Questioning what science enthusiasts might contribute in terms of solutions to global problems, such as climate change and food shortages, the book reimagines standardized scientific modes of inquiry.

Further, it seeks to initiate in-depth dialogues about the roles of possible quantum interconnections between biology and nature. Its concerns involve sustainability, and its approach is philosophical and stream of consciousness. Functioning as a thought experiment, the book suggests useful cultural changes, too, including that more people work to address the needs of the changing planet through new advances in artificial intelligence, blockchain economics, and developing a global grammar.

It dabbles in forecasting universal social changes, like everyone working toward a collective purpose. It uses historical examples, such as how Edison invented the light bulb and so changed the world, for inspiration.

It wonders about contemporary technologies that also optimize potentialities, including about the opportunities represented by artificial intelligence. The text is at its best when it sticks to highlighting the complexity of scientific concepts, particularly when it comes to exploring quantum physics, around which more credible supporting material is named.

The text bounces between abstract and scientific ideas, and most of its concepts are presented in the form of random notes, without much to connect them. Its ideas are often formulated as questions, and its singular style is cluttered. Its passionate hypothetical notions are original, if speculative; a tone of wonderment pervades. Within the text, though, colloquialisms are too common, and emphatic end punctuation is distracting.

Reviewed by Hope Hills May 28, Disclosure: This article is not an endorsement, but a review. The author of this book provided free copies of the book and paid a small fee to have their book reviewed by a professional reviewer.

Foreword Reviews and Clarion Reviews make no guarantee that the author will receive a positive review. Foreword Magazine, Inc. This will subscribe you to all of our newsletters, announcements, and promotional content. For more control over what you subscribe to, head on over to our subscription page. Taking too long?

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