84 Matching Annotations
  1. Aug 2022
    1. explicit documentation of both the execution environment used to run the software and all requirements and dependencies of systems, software, and libraries should be clearly noted in the code and/or readme file (Benureau and Rougier 2018). While time passing can make software obsolete, it also fades the memories of researchers. For that reason alone, it is important to annotate source code to explain the intended operations, which supports reproducibility for the original research team while also supporting future reusers (Benureau and Rougier 2018)
    1. today’s notebook implementations require note-book authors to take various precautions to ensure repro-ducibility, which are exactly the same as required for makingscripts reproducible: a detailed documentation of the soft-ware environment that was used, listing all dependencieswith detailed version information
    1. What I call software collapse is what is more commonly referred to as software rot: the fact that software stops working eventually if is not actively maintained. The rot/maintenance metaphor is not appropriate in my opinion because it blames the phenomenon on the wrong part. Software does not disintegrate with time. It stops working because the foundations on which it was built start to move.
    1. even if the code has been made available, it cannotbe easily run because of changes in the underlyinglibraries, operating systems, and other dependen-cies
  2. Jun 2022
  3. May 2022
    1. Not only this. Try to change the app two years later. Dependencies gone, wrong NPM version, Webpack config depricated and what not.That's why I like to use vanilla JS as much as possible. It will be maintainable years later.
  4. Apr 2022
  5. Mar 2022
    1. L’imitation et l’influence du jeu interactif sont bien mises en évidence dans une étude de Orit Hetzroni et Juman Tannous, de la Faculté des Sciences de l’éducation de l’Université de Haifa (Israël)

      ==>l’échantillon de l’étude est est extrêmement limité, l’étude n’est pas répliqué et elle ne permet pas de retirer de résultats concluants

  6. Jan 2022
  7. canvas.ucsc.edu canvas.ucsc.edu
    1. The Work of Art in the Age of Mechanical Reproduction by Walter Benjamin

      1. Benjamin is part of the Frankfurt School at Institute of Social Studies in Germany.
      2. They are trying to examine the failure of Marxist revolutionary social change.
      3. The idea is that ideology disseminated through mass media are making it very difficult for Marx's prognotication are making it very difficult for social change to occur.
      4. 19th century modernity: mass transportation, factory work, dissemination of capitalism, movement to cities and experience of urban life

       These convergent endeavors made predictable a situation which Paul Valéry pointed up in this sentence: “Just as water, gas, and electricity are brought into our houses from far off to satisfy our needs in response to a minimal effort, so we shall be supplied with visual or auditory images, which will appear and disappear at a simple movement of the hand, hardly more than a sign.” (op. cit., p. 226) Around 1900 technical reproduction had reached a standard that not only permitted it to reproduce all transmitted works of art and thus to cause the most profound change in their impact upon the public; it also had captured a place of its own among the artistic processes. For the study of this standard nothing is more revealing than the nature of the repercussions that these two different manifestations—the reproduction of works of art and the art of the film—have had on art in its traditional form.

      Q: Why does it matter that film minimizes the aura?

      At the time, art reacted with the doctrine of l’art pour l’art, that is, with a theology of art. This gave rise to what might be called a negative theology in the form of the idea of ‘pure’ art, which not only denied any social function of art but also any categorizing by subject matter. (In poetry, Mallarmé was the first to take this position.) An analysis of art in the age of mechanical reproduction must do justice to these relationships, for they lead us to an all-important insight: for the first time in world history, mechanical reproduction emancipates the work of art from its parasitical dependence on ritual. To an ever greater degree the work of art reproduced becomes the work of art designed for reproducibility.7 From a photographic negative, for example, one can make any number of prints; to ask for the ‘authentic’ print makes no sense. But the instant the criterion of authenticity ceases to be applicable to artistic production, the total function of art is reversed. Instead of being based on ritual, it begins to be based on another practice—politics.<br> Ritual: pre-modern timesPolitics: Despite the political painting the art piece will be associated with the aura of original piece of art.

      • Film is not auratic because in film: 1) spaces and times are constructed 2) actors performance is stitched together 3) actors do not share space with spectators 4) multiple points of view 5) appeals to a MASS AUDIENCE and a COLLECTIVE AUDIENCE 6) reveals new aspects of the thing reproduced (time alpse, slow motion).

      How do institutions put the aura back into film?

      In photography, exhibition value begins to displace cult value all along the line. But cult value does not give way without resistance. It retires into an ultimate retrenchment: the human countenance.

      The superstar is a way to put the aura back into film

      The film responds to the shriveling of the aura with an artificial build-up of the “personality” outside the studio. The cult of the movie star, fostered by the money of the film industry, preserves not the unique aura of the person but the “spell of the personality,” the phony spell of a commodity. So long as the movie-makers’ capital sets the fashion, as a rule no other revolutionary merit can be accredited to today’s film than the promotion of a revolutionary criticism of traditional concepts of art. We do not deny that in some cases today’s films can also promote revolutionary criticism of social conditions, even of the distribution of property. However, our present study is no more specifically concerned with this than is the film production of Western Europe.

      *Marx says capitalism produces the seeds of its demise. We can think of that as a guiding principle in which capitalism produces the neorosis that leads Chaplins character into a destructive set of behaviors that stops the Fordist capitalist production in a factory.

      Feelings of belongoing and togetherness and being overhwemed by a mass you want to be a part of , but for Benjamin this is a trynanny where people feel they are in control but they are not really in control. Thus communism replies by politicizing art. Art for art's sake is harmful when put in the service of a facist regime. Art for political progress.

      The growing proletarianization of modern man and the increasing formation of masses are two aspects of the same process. Fascism attempts to organize the newly created proletarian masses without affecting the property structure which the masses strive to eliminate. Fascism sees its salvation in giving these masses not their right, but instead a chance to express themselves.21 The masses have a right to change property relations; Fascism seeks to give them an expression while preserving property. The logical result of Fascism is the introduction of aesthetics into political life. The violation of the masses, whom Fascism, with its Führer cult, forces to their knees, has its counterpart in the violation of an apparatus which is pressed into the production of ritual values.

      Film is not merely a translation of an in-person thetaer performance. Rather film is performing for future audiences and for the director and for cinematrography. This supports the idea that film is a collabroative creation that brings an object into the world.

      One film can be playing multiple times around the world and so this can be distributed on mass scale.

      Film is not merely a recording of reality. Film reproduced new aspects of the things reproduced through slow motion and it brings to light entirely new aspects of matter but discloses quite aspects within them. If Benjamin merely interested in the epistemological possibility of the film to expand our limited perceptual appartus, yes but think about how this reinforces his claim that film moves us away from the aura,...that if we can see unknown aspects by recording it then we can't rely on film to reproduce an original we have to keep in mind that the image is qualitatively distinct from our perceptual access to the thing. So film is not merely a copy of the thing that it records.

      Benjamin flips things and says that maybe film isn't art the way we see an art and this will get us away from the trappings.

      What is Benjamin's definition of art which he is defining with the aura, the transcendence of individual of ritual.

      1. substructure or base: factors that produce commodities and economic relations that result from these concrete aspects
      2. superstructure: culture, law, media that for a Marxist thinker emerges in the way that the economic structure functions; the more media/education/political cosumption that you do the less you are going to understand the conditions of your exploitation and the more you are going to think change is possible.
      3. What role does cinema play in the move from cult and aura to mechanical reproduction? See snapshots.
  8. Dec 2021
    1. AIMOS. (2021, November 30). How can we connect #metascience to established #science fields? Find out at this afternoon’s session at #aimos2021 Remco Heesen @fallonmody Felipe Romeo will discuss. Come join us. #OpenScience #OpenData #reproducibility https://t.co/dEW2MkGNpx [Tweet]. @aimos_inc. https://twitter.com/aimos_inc/status/1465485732206850054

  9. Nov 2021
  10. Oct 2021
  11. Jul 2021
  12. Apr 2021
    1. This project will be great for instruction and portable reproducible science

      This is what I'm aiming for with triplescripts.org. Initially, I'm mostly focused on the reproducibility the build process for software. In principle, it can encompass all kinds of use, and I actually want it to, but for practical reasons I'm trying to go for manageable sized bites instead of very large ones.

  13. Mar 2021
    1. There are currently three implementations of the ActivePapers concept: the Python edition, the JVM edition, and the Pharo edition

      There is only one reasonable approach, and it's not even mentioned as an option here: the browser edition. (I.e., written to target the ubiquitous WHATWG/W3C hypertext system.)

  14. Feb 2021
  15. Dec 2020
  16. Nov 2020
    1. 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.
  17. Oct 2020
    1. 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.

      We desperately need to fix these foundations of science to focus on solid foundations and reproducibility...

    1. 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,

      Science could learn something from this. Science is too far focused on the idealized positive outcomes that it isn't paying attention to the negative outcomes and using that to better define its outline or overall shape. We need to define a scientific opportunity cost and apply it to the negative side of research to better understand and define what we're searching for.

      Of course, how can we define a new scientific method (or amend/extend it) to better take into account negative results--particularly in an age when so many results aren't even reproducible?

  18. Sep 2020
    1. separate the workflow description from its execution.

      Separating a workflow description from its execution is an important aspect of reproducibility.

  19. Aug 2020
  20. Jul 2020
    1. 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.
  21. Jun 2020
  22. May 2020
    1. This tightly controlled build environment is sometimes called a "holy build box". The Traveling Ruby project provides such a holy build box.
    1. 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.
  23. Apr 2020
    1. 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.
      • Prinsip utama yang patut menjadi pegangan para peneliti/dosen masa depan adalah: keinginan pribadi (self-driven initiative) untuk menyebar-luaskan berbagai hasil risetnya secara luas.

      • Untuk itu teknologi digital dan internet harus dimanfaatkan dengan maksimal. Seringkali dosen/peneliti melupakan hal ini, bahwa internet ditemukan untuk mempercepat dan memperluas penyebaran ide.

      • Integritas riset dan reprodusibilitas adalah dua nilai yang perlu ditonjolkan agar relevan dengan kemajuan era internet, bukan hanya menonjolkan nama jurnalnya dan JIFnya.

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

      Integritas riset dan reprodusibilitas adalah dua nilai yang perlu ditonjolkan agar relevan dengan kemajuan era internet, bukan hanya menonjolkan nama jurnalnya dan JIFnya.

  24. Mar 2020
    1. 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.
  25. Feb 2020
    1. 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.
  26. Jan 2020
  27. Aug 2016
    1. 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

      Argument for the reproducibility channel

  28. Jul 2016
  29. Mar 2016
    1. 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.

      sabotaging reproducibility

    2. 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.

      Sabotaging reproducibility.

  30. Feb 2016
    1. 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

      I think this is one of the most outrageous statements I have ever heard.

  31. Sep 2015
    1. Martin has been under pressure to retract the paper for years, including from within his own society.

      Was there not even an editorial expression of concern or whatever they call that?

    2. 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.

      Wow. That is a very strong indictment. Big argument for why independent channels on top of the literature are so important.

    3. but by an outside medical writer hired by GSK

      I'm not sure that ghost writing is a bad thing as long as "writer" is not confused with lead scientist. Yet another strong argument for contributor roles rather than authors. https://www.force11.org/blog/are-we-ready-define-scholarly-commons-thoughts-force2015

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

      Example of the type of harm that lack of transparency can lead to.

  32. Jul 2015
    1. 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.

      Validation statement RRID:AB_1078205 Summary

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

      Validation statement RRID:AB_1078205 No primary control

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

      Validation statement RRID:AB_1078205 Titration curve

    4. 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.

      Omission of primary antibody

      Validation statement RRID:AB_1078205

    5. 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.

      Validation claim

    6. 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.

      Validation statement for RRID:AB_1078205

  33. Jun 2015
    1. 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.

      Definition of reproducibility

  34. May 2015
    1. 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.
    1. Research publication can both communicate and miscommunicate

      Great quote; of course, this statement is true of all communications. We have entire industries devoted to spin.

    1. 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.

      That is rather outrageous that we've known about this since 1959 and have done nothing about it.

    2. 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.”

      Another case for annotation

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

      Nice quote

    1. 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.
    1. “.. 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.”

      Great quote for reproducibility

    2. 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 importance of post-publication annotation. To me, this is the critical missing piece.

    3. 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.

      The essence of science

  35. Apr 2015
    1. 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].

      Another damning statement.

  36. Apr 2014
    1. Reproducibility

      Reproducibility is mentioned in the title of this section, but it is not mentioned elsewhere in the document and I don't see it addressed in what's written in this section.