This project will be great for instruction and portable reproducible science

There are currently three implementations of the ActivePapers concept: the Python edition, the JVM edition, and the Pharo edition

That's why reproducible test cases are so good

Now that Rails has a dependency on Webpack, it then has a dependency on Node.js and Yarn, surprise! Which means we also need to ensure the versions used for those binaries are specific.

People are rewarded for being productive rather than being right, for building ever upward instead of checking the foundations. These incentives allow weak studies to be published. And once enough have amassed, they create a collective perception of strength that can be hard to pierce.

Weber notes that according to any economic theory that posited man as a rational profit-maximizer, raising the piece-work rate should increase labor productivity. But in fact, in many traditional peasant communities, raising the piece-work rate actually had the opposite effect of lowering labor productivity: at the higher rate, a peasant accustomed to earning two and one-half marks per day found he could earn the same amount by working less, and did so because he valued leisure more than income. The choices of leisure over income, or of the militaristic life of the Spartan hoplite over the wealth of the Athenian trader, or even the ascetic life of the early capitalist entrepreneur over that of a traditional leisured aristocrat, cannot possibly be explained by the impersonal working of material forces,

separate the workflow description from its execution.

Poisson distribution can be used in place of other standard curves to determine template concentration, which means that data can be reliably obtained from the same samples across multiple instruments and laboratories.

This tightly controlled build environment is sometimes called a "holy build box". The Traveling Ruby project provides such a holy build box.

In the examples below, we are using Docker images tags to specify a specific version, such as docker:19.03.8. If tags like docker:stable are used, you have no control over what version is going to be used and this can lead to unpredictable behavior, especially when new versions are released.

This all comes as part of a wider global shift towards more open research practices, and the geochemistry community needs to make sure it is engaging widely with these, as well as connected issues like research integrity and reproducibility, if it is to maintain its relevance in the modern research age.

research integrity and reproducibility, if it is to maintain its relevance in the modern research age

For automated testing, include the parameter is_test=1 in your tests. That will tell Akismet not to change its behaviour based on those API calls – they will have no training effect. That means your tests will be somewhat repeatable, in the sense that one test won’t influence subsequent calls.

Nix helps you make sure that package dependency specifications are complete. In general, when you’re making a package for a package management system like RPM, you have to specify for each package what its dependencies are, but there are no guarantees that this specification is complete. If you forget a dependency, then the component will build and work correctly on your machine if you have the dependency installed, but not on the end user's machine if it's not there.

There are major differences in the physicochemical properties of commercially available EGFR inhibitors.

But in the meantime, the paper has been cited in about 500 other papers, many of which may have been cited multiple times in turn. In

Computer says: oops

By contrast, others use it in thepublication process solely to maintain their competitive bid for priority in a line ofresearch inquiry, as a way to sabotage others’ progress. A scientist in an early-career group acknowledged the need to make results reproducible by telling people‘‘the whole recipe of the whole method’’ if asked directly, but then she talkedabout the ‘‘little trick’’ of not including all the details in a publication orpresentation. Like the scientists in a different group quoted above, she mentionedothers’ practice of taking photographs of poster presentations in order then topublish the results first. She said that people, in defense, ‘‘omit tiny little details’’:‘‘But sometimes in the publication, people, just to protect themselves, will not giveall the details. It’s always right, but maybe it’s not totally complete—to protectthemselves. Because your ideas get stolen constantly, and it’s so competitive ifyou’re a small lab.

A more deliberate form of not sharing is the omission of critical details inpresentations, papers and grant proposals so that others will have difficultyreplicating and extending one’s own research.

For one article that we believed contained an invalidating error, our options were to post a comment in an online commenting system or pay a 'discounted' submission fee of US$1,716. With another journal from the same publisher, the fee was £1,470 (US$2,100) to publish a letter

Martin has been under pressure to retract the paper for years, including from within his own society.

It is often said that science self corrects. But for those who have been calling for a retraction of the Keller paper for many years, the system has failed. None of the paper’s 22 mostly academic university authors, nor the journal’s editors, nor the academic and professional institutions they belong to, have intervened to correct the record.

but by an outside medical writer hired by GSK

This is problematic because the article has been influential in the literature supporting the use of antidepressants in adolescents.

It is clear from the use of ES2 and RMG-II cell lines that the Atlas Antibodies ARID1A antibody is specific for ARID1A in both Western blots and formalin-fixed paraffin embedded preparations of human origin and, coupled with the literature evidence, that it is validated in human tissue.

A No Primary antibody control (NPA) showed no staining in the epithelial or nuclear compartment (Figure 3B; Dataset e).

There was no cytoplasmic or extracellular stromal background staining present and the antibody titrated successfully losing the intensity of staining, as expected

Control slides, omitting the primary antibody, were negative except for the ER2 condition in the RMG-II cell pellet where a weak cytoplasmic background could be seen (Figure 2; Dataset d). Thus there was minimal background inherent in the staining procedure. It was therefore determined that the antibody showed specificity for formalin-fixed paraffin embedded tissues and could be run on murine tissue.

Using Western blot and IHC on murine wild-type and knockout tissue we have demonstrated that this antibody to ARID1A correctly stains murine tissue by immunohistochemistry.

It could be demonstrated that the HPA ARID1A antibody showed positive expression in ES-2 cell lines at the expected size of 270 kDa and no staining for RMG-II.

For this paper, we adopt an inclusive definition of irreproducibility that encompasses the existence and propagation of one or more errors, flaws, inadequacies, or omissions (collectively referred to as errors) that prevent replication of results.

Broockman has ideas about how to reform things. He thinks so-called “post-publication peer review” — a system which, to oversimplify a bit, makes it easier to evaluate the strength of previously published findings — has promise.

Research publication can both communicate and miscommunicate

The bias was first identified by the statistician Theodore Sterling, in 1959, after he noticed that ninety-seven per cent of all published psychological studies with statistically significant data found the effect they were looking for.

But while Schooler was publishing these results in highly reputable journals, a secret worry gnawed at him: it was proving difficult to replicate his earlier findings. “I’d often still see an effect, but the effect just wouldn’t be as strong,” he told me. “It was as if verbal overshadowing, my big new idea, was getting weaker.”

The test of replicability, as it’s known, is the foundation of modern research.

The company spent $5M or so trying to validate a platform that didn’t exist

However, validation projects that were started in our company based on exciting published data have often resulted in disillusionment when key data could not be reproduced.

Error rates detected by the double-entry method ranged from 2.3 to 26.9%.

“.. the majority of medical errors do not result from individual recklessness or the actions of a particular group–this is not a “bad apple” problem. More commonly, errors are caused by faulty systems, processes, and conditions that lead people to make mistakes or fail to prevent them.”

Of course I do not knowingly have any mistakes in print. But I could have a mistake out there I don’t know about.

The reason my syllogism doesn’t eliminate science as a paragon of correctness is that – contrary to the popular view about lone geniuses – science is not about individuals or single papers. It is about the community and the total body of evidence. One individual can be right, wrong, a crack-pot, a genius, mistaken, right for the wrong reasons, and etc. But the community as a whole (given time) checks each other and identifies wrong ideas and mistakes.

However, it is worth noting that academic journal publication may ultimately prove to be a red herring, as an indicator of transparency. Academic publishing decisions can be arbitrary, and introduce lengthy delays in access to knowledge. Furthermore, there is a growing body of evidence demonstrating that journals often fall short of the basic expected standards for reporting of clinical trials. It is commonplace to find that primary outcomes have been switched, for example [7]; findings are routinely “spun” [8]; and compliance with reporting standards such as CONSORT is highly variable. When compared with the long and formal structured Clinical Study Reports created for all industry-sponsored trials, academic papers have been shown to be incomplete and inconsistent [9].

Reproducibility