Science 2.0 and Open Access

Science 2.0 and Open Access

  • Rafikh Shaikh 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?
    Rafikh Shaikh

    We have our own portal for sharing and working collaboratively-

  • Alka Rani 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.
    Alka Rani

    Hey Lisa, I understood the question.. My ans was to Riess's raised question that researchgate should prepare the list of journals those have self archiving in the policy. Which I think researchgate has already initiated based on the recent email I have received.  

  • Sean Haley 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?
    Sean Haley

    The amount of data you're generating sounds impossible to document  and a nightmare to analyse practically. labfolder is a great web-based software for precisely this purpose. They use their own servers to store data (in accordance with CFR part 11 and Good Scientific Practice) and there are options for individuals and enterprises in terms of pricing. There's also a free trial available. Here is the link:

  • Kamakshaiah Musunuru added an answer:
    What is the range of percentage similarity of plagiarism for a review article?
    Especially when using a plagiarism detecting software.
    Kamakshaiah Musunuru

    Firstly, there is no science to decide upon. In case if the content is copied it is better to mention about the source. There must be due credits to the respective author. Knowledge is not private but social property. As far as human cognition is concerned, It is highly impossible to get something out of nothing . We should feel happy living in a society where we still respect other's thoughts. If things goes like this, there is no wounder if someone file suite against other claiming that he/she thinks similar.

  • Ahmed Shafqat 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)
    Ahmed Shafqat

    Any views on the performance of new paperwhite for reading PDF 

  • Justin Skycak added an answer:
    Do you use electronic lab books ?
    Do you use a wiki or similar tools for your daily lab work? What are your experiences ?
    Justin Skycak

    I recently made a simple electronic lab book,, that supports collaborative project development and sharing

  • Justin Skycak added an answer:
    How do you organize your paper writing ?
    I used to send out files with Versions (V0.1, V0.2, ... ), but now i switched to google documents (or wave) for collaborative writing. In the end stages I use ResearchGate REstory for synchronizing versions.
    By using google documents no version conflict occurs, however, regarding tables, pictures and so on, google documents is not "compatible enough" for final layout.
    For reference managing we type manually authorYEAR during the google document stage of the paper while in the end stage we use Zotero with online synchronized databases.
    Justin Skycak

    I like to develop my projects on and then draft formal papers using DropBox + Mendeley

  • Justin Skycak added an answer:
    Which E-Publishing Software do you use?
    Tell us which software you use in your daily work for your (open access) e-publishing.
    Justin Skycak

    I use It's as easy as editing Wikipedia

  • Justin Skycak added an answer:
    Online Collaboration
    I am presently engaged in a research project in Calcutta, India, after completing my master course in biochemistry.
    I am going to address a serious topic here especially to higher ranked professionals and also to students of my category.
    I understand the dearth of research collaboration all through out the world between the researchers individually or through institutes/universities. If the research works are shared more then I think science will progress at a much much faster rate.
    Just like if two people share ideas among themselves, the gross idea of each individual increases and thinking of both rises to a higher level and have wider directions.
    Regarding collaboration I know there are some important factors like secret of scientific works until published, publications, individual copyright etc needs to be considered but isn't these points a bit cheaper in front of greater scientific progress? (giving due respect to existing regulations in scientific research).
    It's not only just about collaboration relating a particular topic between two laboratories. what I mean to say is that can't the collaboration level rises to a higher level?
    Can't research or for that matter papers or publications be created by/between researchers sitting far apart from each other but by sharing pieces of individual biological ideas, research works.
    Isn't the pace of scientific progress slow? perhaps one of the reason may be lack of collaborations between researchers.
    I think I have made my views pretty clear by now. I do not want the researchers to deviate from their original works but only want much more collaborations between the scientists performing similar research work. and more research being carried out and shared between individuals especially in the world where all can be easily accessible through world wide web, that is internet.
    why can't a PhD scholar apart from doing his/her own work also contribute to/ collaborate through internet with other members to give rise to new work in similar or related fields?
    My direct issue is that why can't groups of group members be formed and share their dry lab work or/and wet lab (as per time, conditions and infrastructure permits) together to give rise to new publications and thus contributing very faster to scientific world. Does it always need to be a part/member of same lab?
    why can't an online forum/ group be formed where the datas of the experiments of individual researcher may be shared may be in a secret way for particular experiments and there is a guide supervising it and in the same way publications can also be made.?
    I have written a lot.
    I want views, discussions and suggestions from scientists as well as students about how this can be conducted efficiently and it's pros and cons.
    Justin Skycak

    I agree with you. I think we need a centralized project development site where researchers can not only share but also develop, their projects in a collaborative fashion. I recently made a site,, that does this; hopefully it catches on

  • Justin Skycak added an answer:
    How to find negative data that helps you to avoid performing the same experiment twice?
    As a scientist I am most concerned about not wasting time.

    Given that, at any given moment, other scientists (somewhere) are working on projects that are similar to our research, it is very likely that parts of our results will be also similar. Experiments work (hypotheses are proved) or do not work (hypotheses are disproved). We take it for granted that positive results (experiments that worked and prove something) will be published at some point in the near future (be it by us or by others). Publication of such experiments is hard enough, takes time and presently peer-review is organizing the publication process.


    Importantly though, what we will not and will, probably, never know is this: which experiments did not work or did disprove a given hypothesis. Such knowledge would be very important for us, indeed. Because it will certainly be helpful to know (before starting out on a new project or deciding on a direction to continue a running project) that somebody has failed (somewhere) on the same or a related project. This would save not only time but also resources.

    Maybe, some negative data will be published. Maybe. The reality is that editors do not like to "waste" space in their journals. Where to go then? Increasingly, comments on publications are allowed but obviously one has to go to the journal, to the article and to the comments section. But does your failed experiment have anything to do with the paper you are commenting on? Alternatively, you might talk to other scientists at meetings. Or you might hope that some website like ResearchGate or will connect you with scientists and their (negative data) knowledge. Well, this is the idealistic approach but right now, I do not see an incentive for scientists to share such (negative) data on these websites.

    Therefore my question: What format, beyond the comments section of journals or the establishment of journals that publish negative results, can you think of to extract the hidden knowledge of failed experiments from your fellow researchers. Knowledge, which might allow you to fine-tune or to abandon an approach to a scientific question because somebody else has asked it, performed experiments and gave up on it for good reason.
    Justin Skycak

    Perhaps a collaborative research database, where researchers can log project developments and not just the final outcome, could be of help. A new site that serves this purpose is

    I think researchers can be unmotivated to draft a write-up of negative results; however, if researchers are publicizing info throughout the whole research process, then a write-up will exist regardless of whether the results are positive or negative.

  • Justin Skycak added an answer:
    A talented young student is enrolling in your research group, what supporting tools would you recommend as a starting kit?
    To be more specific, let us cover, at least, the following segments: (a) planning and task management tools, with emphasis for web-based ones; (b) diagraming tools to convey, discuss and share ideas; (c) co-authoring and referencing management tools.
    Justin Skycak

    A collaborative research database, such as, could be of help.

  • Justin Skycak added an answer:
    How can we use social media to amplify our research and knowledge sharing?
    Here is a presentation slides to a 1/2 day seminar I will be giving at Universiti Sains Malaysia (USM) on the 28th June, 2013. Your thoughts, experiences and ideas on this topic would be highly appreciated. Still in ultra learning mode :)
    Justin Skycak

    I recently created a site,, where researchers of all levels can collaboratively develop and share projects. It's not busy yet (and it's only a month old), but I hope that it will be a useful tool to amplify research and knowledge sharing.

  • 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

    I have a methods paper on this exact subject in review at the moment and a practical application manuscript also in review. Send me a message if you would like to see drafts. In summary (for environmental sciences systematic reviews):

    1. GS only displays the first 1,000 search results and the ordering of these results is not clear. GS is therefore not suitable as a standalone resource and it's use in a SR is not in keeping with the need for transparency and repeatability.

    2. Title-only searches obviously yield fewer results, but a higher proportion is grey literature than full-text results. So the utility of and ideal search settings in GS depend on what you are using GS for: grey or academic. Grey literature occurs mostly around the 200-300th results (pages 20-30) so searching the first 50-100 results (as often seen in env management SRs) is a poor practice if grey literature is the target. 

    3. We have developed a method to download and extract as citations these first 1,000 results, making the search process transparent and updatable. (request our methods paper for this process)

    4. Similar searches in GS and Web of Science yield poorly overlapping results (especially where results are far larger than the first 1,000 displayed). GS is therefore a useful addition to traditional searching.

    We conclude that GS is a useful addition to traditional SR searches, and that new methods allow transparency and updatability using GS.



  • Rizwan Faisal added an answer:
    Free Manuscript submission
    Dear All,

    Please suggest me any scientific journal to submit free manuscript.
    I have written a paper on HIV coreceptor variation but unable to publish it as idont have enough financial support.

    Rizwan Faisal

    archives of iranian medicine is an impact factor free journal

  • Igor I Katkov 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?
    Igor I Katkov

    Ma-a-a-an, this discussion will last longer than some sacred books heroes or avatars (I am not talking about the movie but about  ;Prof. Dhanvantari -))

  • Sadek Amami 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
  • Jeroen Bosman added an answer:
    What are the best scientific papers on impact of science 2.0 (open science, citizen science, data-intensive science)?
    I'm looking for evidence that the science 2.0 really changes the way we do science today (in positive and negative sense). Can we prove that the change already took place? If yes, in what areas? Does it happen only in natural sciences? More information on our study on
    Jeroen Bosman

    Try this freely available book:

  • Fidele Ntie-Kang 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?
    Fidele Ntie-Kang

    -RG also creates a forum where young researchers can be mentored by more experienced researchers.

    -It creates a forum for exchange of data and knowledge between researchers who may never meet in real life.

  • Rasheed A. O. Shidi added an answer:
    How to publish a scientific paper?
    This is a platform where we got ideas from wide range of researchers. One of the challenge in science is how to publish your work. It has been observed that some researchers have depth knowledge in their field and working hard from number of years, despite all hard work they are unable to publish papers. Though satisfaction is important but research publication is also important. This way your research reach to your target audience. I would appreciate if you advice how to publish paper in scientific journals. Please write problems you are facing in publishing your research, it is possible that some of experienced researchers may provide solution to your problems. Experts' are requested to give their advice on this subject.
    Rasheed A. O. Shidi

    Dear Nguyen, I`ll rather suggest above all, to first try paper journal of which you are linked to at your professional area of practice.

  • Mpho Keetile added an answer:
    Does anyone have experience with publishing in the Journal of AIDS and Clinical Research form the proteomics group?
    I cannot find it in the official lists of Thomson Reuters or similar databases and the impact factor listed on their webpage is based on citations of their articles but an unofficial one.
    Mpho Keetile

    I have my article accepted for publication in this journal, and publication fees are unaffordable,am i wasting my time by paying and publishing in the journal

  • Mamoon Rashid added an answer:
    Dear all
    How we can calculate the rpm from xg in centrifuge? Please help me
    Mamoon Rashid

    Most of the centrifuge instruments are equipped with modes to switch between RPM to RCF. Do the math, but please check with what the instrument displays. 

  • Rishabh Shrivastava 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?

    Rishabh Shrivastava

    Dear Stefanie,

    Do you suggest that altmterics is associated with social media metrics only? Because most of the studies have been conducted on Mendeley readership and CiteUlike etc. I find they are not pure social media sites. I think popular social medi sites such as Facebook and Research Gate happen to be less explored. Won't it be too early to call it social media metrics?

  • Gregg W. Etter added an answer:
    Would you do an AudioSlide presentation for your published article on ScienceDirect?
    Some journals on ScienceDirect started to offer this new service, How would that reflect on the merit of the article?
    Gregg W. Etter

    I watched an AudioSlide presentation on identification of human remains in a mass casualty incident the other day.  It was a little dry, but extremely informative. I got something out of it and thought that my time was well spent.

  • Susan Mazer added an answer:
    I so appreciate this opportunity to join you in this dialogue!! I have been involved with a new open access journal that has not yet launched.
    How do OA journals deal with liability issues such as plagiarism or misinformation in an article submitted...if there is little budget? Is there any history that points to likelihood of any legal issues arising?
    Susan Mazer

    I look forward to learning more about what you are doing and what your students are doing.  My husband, Dallas Smith, comes to India every year with "Mynta," Swedish Indian-Jazz fusion musical group.  We have been to India many times and have Indian culture around us every day!  Dallas studies with Ali Akbar Khan and continues to play the bansuri.  We have much to talk about!

    Our work in healthcare draws upon all of our musical experiences.  I am a professional harpist for many decades!


  • 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

    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.

  • 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

    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

    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.

About Science 2.0 and Open Access

Information exchange on Open Access topics in scientific publishing

Topic followers (14,290) See all