Science 2.0 and Open Access

Science 2.0 and Open Access

  • John Tainer added an answer:
    Would you publish your negative results? If no, why?
    Do you agree with the article below regarding the value of negative results?
    John Tainer · The Scripps Research Institute

    There is always the pressure for people to do what they are rewarded for doing. So it can help if promotions and raises are based upon honest and open efforts and publication rather than always having the most desired outcome. We should work to insure that researchers are rewarded for positive and negative results that are truly informative and useful. Negative results may be uninformative in many cases and there are many reasons for experiments to fail that do not necessarily provide much useful information. Obviously negative results in some cases such as drug trials can be super informative. So the issue is not so much positive or negative results as it is providing complete useful data. 

  • Niranjan K. Naik added an answer:
    How is ResearchGate dealing with copyright issues when posting our papers?
    I am wondering if there are any copyright issues when we post our published papers on ResearchGate? Is there any rule we should follow or we can simply upload the papers and hope that we do not really break the publisher's copyrights. I will be more than happy to know more about this.
    Niranjan K. Naik · Indian Institute of Technology Bombay

    A link to the journal website can be given. Individuals can access to the article through their library.

  • Abd El-Aziz Ahmed added an answer:
    What kind of software and online services are research labs using for social collaboration, and project, knowledge and lab management?
    There is a wide variety of cloud-based and locally installable software tools available for potentially enhancing the output of a research lab. These include (with examples): project management (Basecamp), wikis (Confluence), microblogging (Yammer), document management (Skydox), reference management (Mendeley), scientific collaboration platforms (colwiz), general online collaboration platforms (Zoho), e-notebooks (Labvantage), laboratory management systems (CambridgeSoft) and instant messaging (Skype).

    We are currently looking to improve the way we work in our lab regarding communication and data management. Being an academic research unit of about 80 people studying nanophotonics, we are currently generating huge amounts of data on network drives and paper notebooks, and communicating in a semi-random fashion. Everyone is using their own tools. Clearly there is much room for improvement, or is there?

    So, the question is, what kind of software services are other labs using? How did you identify the needs of the users, selected the tool and got everyone to use it?
    Abd El-Aziz Ahmed · Cairo University

    Now, we are using DropBox

  • Karin Zwiesler added an answer:
    How can I determine if a journal in which I have published supports "self-archiving"?
    I would like to provide copies of papers I have published, but I do not wish to violate the rights of the journal or the copyright laws. I would welcome the experience others have had in answering this question
  • Rahul Alam added an answer:
    How does the search for health information affect health literacy?
    Looking for any comments and views on how health information seeking will affect health literacy, if it does so significantly, especially in the contexts of new media.
    Rahul Alam · The University of Manchester

    Hi Mohammad,

    Interesting question - but i think that health information seeking will have little direct short-medium term impact on health literacy. I think that the converse is more likely where health literacy impacts on health information seeking. To what extent is the question and leads us to the chasm of what's being done to address poor health literacy across the globe.

  • What is the range of percentage similarity of plagiarism for a review article?
    Especially when using a plagiarism detecting software.
    Prof. (Dr.) Deepshikha Bhargava · Amity University

    The matching text found is not an assessment of whether work has or has not been plagiarised. The plagiarism checkers can check the similarity index of the submitted paper and the suspect sources. Ideally the similarity index below 15% is acceptable but it depends upon the guidelines and the policies of specific conference/publisher/journals. Some authors also change the words a little or using synonyms but retaining the author's essential thoughts, sentence structure, and/or style without citing the source is still considered plagiarism. The Originality should be in the ideas and sense of honesty. Suggestion is also to check your papers on Licensed software or Copyright tools/websites, Freebies are not as authentic as Licensed/ copyright versions. Where ever have a doubt.......CITE.

  • Lars Gille added an answer:
    Has anyone experience in reading scientific papers with e-readers (kindle)?
    Guess, this is not a very subject specific question. However: I don't like reading papers on my computer screen, but don't want to print them out. What is your experience with e-readers for paper reading (esp. the kindle)? Is there a possibility to mark text passages (e. g. underlining)
    Lars Gille · University of Veterinary Medicine in Vienna

    In the meantime I got the DPT-S1 (not to be confused with the Sony PRS-T1). It is great  for reading PDFs because it is life size with its 13.3 inch screen. The annotation function with the pen is really fast and fairly accurate (after manual calibration). The PDF with handwritten notes, highlights and sticky notes can be easily transferred to PC via a WebDav cloud account. Furthermore, Worldox provides some tools on his web page for this reader by which you can easily convert your word files to PDF and send it to your cloud account by simple drag and drop. This way it takes about 2 min to have your documents on the reader. 

    Of course there are also some limitations of this product:

    - price

    - limited availability outside US and Japan

    - you can not annotate in zoom mode

    - you can not move files between different folders on the reader without PC

    Nevertheless, this devices unique in its class. Compared to my Pocketbook Pro 903 it is a huge progress.

  • Elisabeth Lex added an answer:
    Does anyone have experience with research on altmetrics - which datasets?

    I would like to get an overview which datasets the community uses when working with altmetrics and whether they are publicly available. Also, are there any "standard" datasets? Do you think such datasets would drive research further?

    Elisabeth Lex · Graz University of Technology

    Thanks Stefanie, this is very helpful!

  • Jason Gao added an answer:
    What kind of presence, if any, should a research lab have in social media?
    Our lab has an up-to-date website with a nice news section. However, it seems certain that most of our target audience will not visit the website regularly, so the readership of our news is very limited.

    The university is active in LinkedIn, Facebook and Twitter, but naturally only shares the most important news. Therefore it seems that we should be active ourselves in sharing links to our news in social media. Some individual researchers do promote their own research online, but a concentrated lab-level effort would seem more effective.

    We have considered setting up a LinkedIn group for our lab. This would be used for sharing links to our website news, new papers and job opportunities. A joint SlideShare account also seems worth the effort. Other obvious alternatives are Twitter and Facebook, and of course ResearchGate.

    Do you think this would work, or would there be a better way?

    As a motivation, increased publicity potentially brings new contacts, collaborations, projects, research, funding and so on.

    Edit: Prof. Ravi Sharma nicely clarified the motivation for participating in social media below:

    1.Creating awareness,
    2. Popularising/sharing of services/ products/land mark achievements/papers/articles/presentations etc.
    3. Attracting desired human resources
    4. Networking among participating scientist resulting in better circumstances for productive and collaborative research & development - institutional as well as individual levels.
    Jason Gao · Peking University

    I'm also interested in this topic, and currently I'm doing the market survey about lab social network condition. We have made a questionnaire, hope you can fill it and speard the questionnaire link to other faculty and phd. Great thanks! The questionnaire link:

  • Curro Garcia added an answer:
    A new monoclonal antibody to a cell surface receptor has been produced in the laboratory. When the cells are incubated with antibody solution, cells get activated instead of inhibition implying failure of blocking of receptor by antibody. What could be the reason for this result? How could you possibly modify antibody to prevent the activation reaction?
    Curro Garcia · Universidad de Cádiz

    Antibodies could either block or activate depending among other things on the position of the epitope they recognize. There is little you can do on the antibody to change that. Sometimes activation depends on the ability of the antibody to bring together two receptors and in those cases digesting your antibody into Fab fragments may helps. You could raise antibodies against the ligand of the cell surface molecule you want to block.

  • Doaa Altarawy added an answer:
    What is a good reference managing software
    i've checked a lot of these reference managing software, but what shall one see before using one.
    With all the options available in the market, which one addresses to all the requirements of a good reference manager.
    are open source alternatives any better than their premium peers.
    pls advice
    Doaa Altarawy · Virginia Polytechnic Institute and State University

    I vote for Mendeley too.


    free, good in importing folders and parse them automatically, good bibtex output, works on the web, desktop or tablet, networking, attaching pdf files, sync between devices.


    PDF editor that comes with the desktop version has very basic annotation features. As it is intend to be for scientists, it is expected we will need much more features (but a nice thing that it allows open in external editor)

  • Tze Leong Chan added an answer:
    Hi, I am a science writer from Brazil. I am going to write about Researchgate, so I would be glad if could answer me:
    Why have you enjoyed to this network and what are the major bennefits from it?
    Tze Leong Chan · Universiti Teknologi Malaysia

    Dear Sofia

    RG allowed me to collaborate and network with other researchers on new research projects. It provides me an open and free platform across researchers across the world to get their feedback, opinion and suggestions in response to my questions. The more I contribute, the more I know the world gets more informed, is the best benefit provided by RG. . 

  • Mardene Rosalee Carr added an answer:
    How comfortable are you using Open Educational Resources?
    With the high cost of journals and electronic databases many people cannot afford to purchase. Open Educational Resources are now an alternative, do you trust these resources?
    Mardene Rosalee Carr · University College of The Caribbean

    Thanks for all your contributions to this question.   No doubt there is a lack of awareness because there are lots of excellent resources available via this medium.

  • Vijayakumar Rajendran added an answer:
    What is the impact factor of Journal of microbial and Biochemical technology
    Can any1 tell what is the impact factor of Journal of Microbial and Biochemical Technology?
    Vijayakumar Rajendran · North Eastern Hill University

    Now it got impact factor of 2.16 and one can see in the researchgate itself.

  • Bhupendra Desai added an answer:
    The advantage of sharing your negative results
    An article on the benefits of sharing negative data...
    Bhupendra Desai · Indian Institute of Technology Roorkee

    What means by negative results?????? results not as per your requirement, or thoughts, or not what you were expecting !!!. Why????? and research started. Newton's negative thought,'Why apple does not, go up ', invented force of gravitation.Means negative results are having equal, or some time, more importance than positive results, in fundamental research work with mathematical modelong. Researchers should not hesitate to published, negative results, it may give thoughts for further research to our friends.

  • Amin Zarghami added an answer:
    journal impact factor
    if theris a one how can gives me the latest journal cited report jcr of ISI thomson.
    Amin Zarghami · Babol University of Medical Sciences

    Hi there,

    The latest JCR finally released after one month delay by the Thomson Reuters company.

  • Ivo Grigorov added an answer:
    How do you use #OpenScience to feed the "Publish or Perish" needs for measurable IMPACT?

    Scan the questions sections for #OpenScience, #Science20, #OpenAccess and you will notice that the vast majority by far, are spending significant Q&A on what is wrong with Open Science, what does not work, and what could (or has) horribly gone wrong. Makes you wonder how high the h-index on those questions gets, and how representative that is of reality.

    Although exposing fraud, plagiarism, bad publisher service, and poor quality is essential to prevent other falling victim, it is hardly as inspiring or motivating. Actually, it can give the wrong impression to the novice, and be dangerous.

    So, let's balance the discussion and focus on the what works, by apply the scientific method to gauge the positive side of #OpenScience (if any). There are many shining examples of how #OpenScience can boost your career profile, on the way to that tenure.

    OS practioners, we know you are out there, so don't be shy and tell us how you integrate OS in your daily workflow, and in what measurable ways does #OpenScience contribute to your profile and impact?

    Ivo Grigorov · Technical University of Denmark

    Hi Cornelius, you are dead right!

    But when it comes to making OS part of the daily research workflow, we the convinced, have to demonstrate to the sceptics that OS can contribute to what they dearly care about (e.g. imapct the way it is measured now, IF, citations, things that count towards tenure, and better chances for funding to estabish and sustain a research group).

    If we believe in OS, we have to advocate for it in more than just our belief for it. We have to apply the scientific method and offer quantitative effidence that what we believe can contribute to what the sceptics care about.

    Many thanks for your contribution!


  • Jess H. Brewer added an answer:
    Is reproducibility really essential to science?
    See abstract of the paper. Obviously this is posted in response to the criteria stated in ResearchGate's Open Review introduction. I would be pleased to see ResearchGate take over and do it right, but this notion of evaluating strictly on the basis of "reproducibility" is as silly as counting Facebook "likes". (IMNSHO)
    Jess H. Brewer · University of British Columbia - Vancouver

    @Balázs: I think we are both running out of new things to say here. Sort of a "quibble-off".... I should just let you have the last word, but I can't help one last quibble: it seems to me that an individual theorist can never use your version of The Scientific Method, because the required experiments or fresh observations may not be possible for that one person to perform; in that case a theory becomes "scientific" only after its predictions are thoroughly tested by others, sometimes after the original theorist is deceased. This seems awfully retroactive for a "Method".

    I regard my original Question as "answered"; RG should revise its criteria in the Open Review tool! Meanwhile we have raised a number of more philosophically interesting questions; anyone feel like enshrining them in new Question threads?

  • Ivo Grigorov added an answer:
    Which online tools do you use for open science?
    Do you share your research ideas openly with others? Do you make your research process transparent? Do you make your research findings accessible?
    If so, which online tools are useful?
    Ivo Grigorov · Technical University of Denmark

    A great collection of working examples for Open Notebook Science to support building a high impact research profile.

    The page will include a vision paper (in draft) on ONS and how to engage the younger research generation.

  • Nader Ale Ebrahim added an answer:
    Would you like to give open access to your papers?
    More and more open access journals are emerging. Would you like to submit your paper in such journals? Additionally, open access is also provided as an option in a lot of conventional journals, which can surely increase the visibility of your paper. Thus, do you prefer this option? Finally, does your institute or project pay the costs?
    Nader Ale Ebrahim · University of Malaya
    Somehow yes. Recently I have published an article entitled "Effective Strategies for Increasing Citation Frequency" which is available online on . You can find over 33 different ways for increasing the citations impact.
  • Linas Balciauskas added an answer:
    What is the job of an editor, and how does that relate to the apparent reduction in quality of academic writing?
    As a researcher and therefore a reader of papers, I often encounter poorly written papers, full of grammatical and spelling errors. Of course, one cannot fully blame the authors -- many researchers are not native english speakers (myself included), and some only speak english at a very basic level, or not at all. However, some publication platforms (journals, magazines, transactions and so on) have editors listed: a group of people that tends to change per issue or a set of issues. My impression was that editors edit the papers for publication, mainly focussing on formatting and language (with feedback from authors, of course).

    However, reading papers from a Lecture Notes in Computer Science issue, I'm quite certain that language isn't part of what editors do. Some articles, especially those that come from Workshop and Conference proceedings, often lack editing, sometimes to the extent that the paper is (for me, at least) no longer understandable. However, I've even noticed this problem for Journals. In addition, my reading experience seems to indicate that the problem is increasing, which would be a rather troubling fact that could be addressed by editors or by reviewers. I expected this to be addressed by reviewers; the quality of text is important to the correct communication of information. On the other hand, it may be unfair to non-native speakers to consider language in the review process.

    Thus, my question actually consists of two parts:
    1. What is the 'job description' of an editor?
    2. How can the research community as a whole (authors, reviewers, PCs, readers, editors, ...) improve the situation?
    Linas Balciauskas · Nature Research Centre
    I think, authors are the pillows of any journal, not the editor. Editor just make some judgements... When authors are poor, I mean their papers are poor, then no chance that Editor will help.
  • Rachel Y Lei added an answer:
    What do you think about the idea of common open access for scientific publications?
    In the era of common internet communication seems to be normal that knowledge (science) treated as common human heritage and accessed for all, might be the best tool for breaking several barriers and making global progress.

    Costs of electronic publications are incomparably lower than those in traditional paper production. Meanwhile only small part of renowned editors decided to give opportunity to open access for scientific publications, other as Springer proposes to open choice option after payment of 3000 US$ fee for one publication. Most authors in the world are employed in different state universities, where salaries are dramatically low, and no chance to pay such costs by them.

    Should governments support these costs of editors (if are really necessary) to open access to knowledge for their citizens? Is the place for common open access publishers competitive for monopolised market of high ranked journals? Should governments initiate discussion about common open access for science regulations, instead of ACTA law conspiracy?
    Rachel Y Lei · US Oncology
    It seems to me that just as many conference/societies charge different rates for registration/membership based on presumed income levels (and offer scholarships/assistance for participants from lower income countries) journals should offer similar sliding-scale arrangements so that they can cover operational costs while giving more access to lower-income researchers and institutions and garnering more potential submissions (researchers aren't likely to submit to journals few of their colleagues will be able to read).
  • Rubén Barone added an answer:
    Is the US leading the way in Open Access?
    Below is an interesting discussion relating to the Federal Research Public Access Act (FRPAA) and how to help it become law. I'm interested in others experience in recent years of open access and what different governments are doing to implement it?
    Rubén Barone · Independent Researcher
    In Spain there is a very good digital library for Botany:
    On the other hand, many journals are in Open Access form in Internet, e.g. Ardeola (Ornithology): and Anales del Real Jardín Botánico de Madrid (Botany):
    But there are many other journals also in OA (on Geology, Botany, Entomology and Zoology).
  • How do you organize your experimental data?
    Science is all about data, but we scientists (at least biologists) are not specialists of data. I spend so much time organizing data, and wonder if we can use Ruby on Rails-like approaches to organize, analyze, and visualize data?

    I want to handle my data in a simpler way. I guess I could use MVC, DRY or RESTful approach.. That way, other people can understand your data more easily. Does anyone use rails in research?
    Pedro Antonio Barrientos Loayza · National University of Cordoba, Argentina
    The best option for the question that you do is the following:
    1 - Freemind. Allows a map and can you order it to suit the needs and then export it to a document (odt or html..)
    2 - Docear. Academic is a very useful suite that combines freemind and JabRef, but you must have a version of PDF viewer installed so you can go by the marks or comments.
  • Vladimir S. Myasnichenko added an answer:
    What is the current role of Wikipedia in Medical Knowledge?
    The role of social media in building scientific and medical knowledge has been changing rapidly, and seems to be increasingly reliable, usable, and accepted within the field. How do you use Wikipedia in your medical work and how do you recommend others (especially students) use this resource. Also, does anyone have experience writing medial articles for Wikipedia? If so, do you have any advice to offer on the process?
  • Neal Haddaway added an answer:
    Google scholar for systematic reviews: what limit on search returns?
    Are any researchers who are undertaking systematic reviews also adding a search of google.scholar? And if so, what numerical limit are you putting on results that you inspect? In some earlier trials, I found that scholar returned in the order of at least 10x more results than did the more usual sources (like Medline) which I feel would then artificially distort the number of excluded articles in your flow diagram of articles to be included.
    Neal Haddaway · Kungliga Vetenskapsakademien
    Hi Andrew,

    One option is to restrict your Google Scholar search to titles only and to use scraping software to extract all the search results for separate screening. It may not save any time at all, but it does increase transparency and repeatability. Data Tool and are low cost and free bits of software for just this purpose, although gets blocked after about 500 searches if you're not careful.

    For environmental management SRs we find typically between 5 and 30 % of GS results are grey literature, so it is worth doing, depending on the subject. We see a lot of authors just screening the first 50 results, though, which is just lip service in my opinion.

    On a more technical note, according to Google, GS catalogues absolutely anything that fits 4 key rules - title, authors nearby, references section and a PDF (if I remember correctly), so there shouldn't be any bias it what it shows, just the order it displays them. By using title search you can dispense with order and perform your own searches of the results that you find.


About Science 2.0 and Open Access

Information exchange on Open Access topics in scientific publishing

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