Scientific Visualization

Scientific Visualization

  • Sidharth Thakur added an answer:
    Is there any recommended software to visualise articles/papers/references when conducting a systematic review or meta-analysis?

    I'm planning on conducting a systematic review and meta-analysis. For this I would like to visualise the relationship between different papers in how they cite each other (think of it like Facebook friend wheel) to see if there are clusters (eg. American journals cite other american journals) and then see if their main findings also correlate (to see if researchers are more inclined to cite other supporting papers rather than findings that contradict your own results).

    I would also like to be able to add parameters like Impact Factor, Almetric and such in evaluating the quality of my included articles in my systematic review. Is there a tool that automatically adds such information? Does Mendelay or EndNote have that function? Or do I have to find it for each paper using JCR?

    All this functions does not necessarily have to be in just one software.

    Any tips on visualisation tools are greatly appreciated, as long as they are simple to use. I realise this can probably be done in a spreadsheet and then write code in R but I'm looking for a simpler solution with a less steep learning curve.

    Sidharth Thakur

    Hi Rasmus,

    You might want to check out the paper linked here, presented recently at IEEE Visualization conference. The authors present a tool called SurVis for analysis of document collections. I don't think they build citation networks, but should be worth checking out.

    There is a huge body of work on citation linking and visualization (early work by Chaomei Chen & Katy Borner). Search IEEEXplore for visualization of documents and you might find other relevant papers.

    I am building an app for deriving insights from documents and collections of documents. My app is still in development, but I'll be happy to share with you - send me a message.



    • [Show abstract] [Hide abstract]
      ABSTRACT: Bibliographic data such as collections of scientific articles and citation networks have been studied extensively in information visualization and visual analytics research. Powerful systems have been built to support various types of bibliographic analysis, but they require some training and cannot be used to disseminate the insights gained. In contrast, we focused on developing a more accessible visual analytics system, called SurVis, that is ready to disseminate a carefully surveyed literature collection. The authors of a survey may use our Web-based system to structure and analyze their literature database. Later, readers of the survey can obtain an overview, quickly retrieve specific publications, and reproduce or extend the original bibliographic analysis. Our system employs a set of selectors that enable users to filter and browse the literature collection as well as to control interactive visualizations. The versatile selector concept includes selectors for textual search, filtering by keywords and meta-information, selection and clustering of similar publications, and following citation links. Agreement to the selector is represented by word-sized sparkline visualizations seamlessly integrated into the user interface. Based on an analysis of the analytical reasoning process, we derived requirements for the system. We developed the system in a formative way involving other researchers writing literature surveys. A questionnaire study with 14 visual analytics experts confirms that SurVis meets the initially formulated requirements.
      IEEE Transactions on Visualization and Computer Graphics 11/2015; 22(1):1-1. DOI:10.1109/TVCG.2015.2467757
  • Paulo Carvalho added an answer:
    What are the methods of information visualization?

    Whether there is classical textbooks, lectures on methods of data visualization

    Paulo Carvalho

    In deed, it seems to be a very interesting course.

    Thank you Christos.

  • Ricardo Matias added an answer:
    Can anyone suggest an open source software to make scientific diagrams?

    I am always fascinated by the kind of diagrams that people publish in Cell, Nature, Science etc.. I want to get such a software that can help me in my research.

    Ricardo Matias

    Hi Ajay,

    Data visualisation is in fact a critical issue when communicating research results. Most of the times our research data is (poorly) presented through a simple table. We definitely need to push our competencies on data visualisation and implement workflows that are able to add value and help disseminate our research.

    Here are some free tools that I hope can help you presenting your research more effectively:

    + 2 more attachments

  • Jochen Wilhelm added an answer:
    How to elegantly show multiple significant differences between groups on a bar graph?
    I have measured gene expression across eight time points, and multiple comparisons show many differences between the time points. I'd like to indicate these significant differences on my bar graph. Usually I would draw a line above the relevant bars and put * or ** above the line, but there are so many differences that the lines would become unwieldy and I feel my graph would just look too messy! Any suggestions? Should I just relegate the p values to a table?
    Jochen Wilhelm

    I see. So you can possibly take initials or abbreviations of these interventions, like

    D Significant difference from Dolomitrin-treatment
    M Significant difference from Melomycin-treatment
    Pa Significant difference from Palatosan-treatment
    Pi Significant difference from Parsitin-treatment

    and so on.

  • Thales Sehn Körting added an answer:
    Experience with using visuals to communicate your research.
    If you are willing to publicly share your experiences, I am very interested to hear your thoughts on the use of visual communication for scientific research. Specifically, I am interested in learning:
    - your thoughts on the importance of visuals
    - the type of software you use to create charts, graphs, schematics, illustrations
    - how much time you spend creating these visuals
    - your thoughts on the value of outside expertise to help you create your visuals
    Thales Sehn Körting
    in my opinion visualization is a very important topic.
    When we see some presentations in conferences, symposiums, etc., it is common to see that lots of people don't care with a good presentation, or good ways to display data.
    However, I have an youtube video that shows how to create a 3D animation of a scatterplot. Maybe it can help.

    Please take a look at:

  • Cayetano Santos added an answer:
    Any good experiences with Matlab alternatives?
    I am evaluating various Open Source tools for use in EE resarch. Few interesting ones would be Octave, SciLab, Python with Numpy and SciPy. Anyone care to share experiences, good or bad? Any other suggestions?
    Cayetano Santos
    Here you can find an interesting report
    "Comparative Evaluation of Matlab, Octave, Scilab and others"
  • Bernard André Alain Chabot added an answer:
    How can I download your visualization ontology?
    I've tried to upload your visualization ontology : in Protégé 3.5, but I encountered a error. Did you check such a import?
    • Source
      [Show abstract] [Hide abstract]
      ABSTRACT: Research papers are published in various digital libraries, which deploy their own meta-models and technologies to manage, query, and analyze scientific facts therein. Commonly they only consider the meta-data provided with each article, but not the contents. Hence, reaching into the contents of publications is inherently a tedious task. On top of that, scientific data within publications are hardcoded in a fixed format (e.g. tables). So, even if one manages to get a glimpse of the data published in digital libraries, it is close to impossible to carry out any analysis on them other than what was intended by the authors. More effective querying and analysis methods are required to better understand scientific facts. In this paper, we present the web-based CODE Visualisation Wizard, which provides visual analysis of scientific facts with emphasis on automating the visualisation process, and present an experiment of its application. We also present the entire analytical process and the corresponding tool chain, including components for extraction of scientific data from publications, an easy to use user interface for querying RDF knowledge bases, and a tool for semantic annotation of scientific data sets.
      To appear 9th International Joint Conference on Computer Vision, Imaging and Computer Graphics Theory and Applications, Lisbon, Portugal; 01/2014
    Bernard André Alain Chabot
    OK. It works fine. Thks !
  • Giovanni Pintore added an answer:
    What's a good visualization tool for a presentation?
    I am searching for a good visualization tool for presenting my research results in a conference. Do you have any fancy tools in mind?
    Giovanni Pintore
    I suggest Powerpoint too
  • Nancy Rodriguez added an answer:
    Which free software would you recommend for high quality 3D scientific visualisation?
    I use Paraview and have experimented with Mayavi for 3D visualisation (volume rendering, surface plots etc.). I find Paraview can be lacking in quality at times and Mayavi has been difficult to use - are there any alternatives people could recommend?
    Nancy Rodriguez
    VTK is also a widely know software for visualization


  • Roy Trevor Williams added an answer:
    How important is storytelling and visualization for your science?
    Two weeks ago, I attended two interesting presentations, one of a British SME (shoothill) on visualizing scientific data for the public (for example applying a technique known as Deep Zoom), the other of the Polytechnic University of Milan on using NASA world wind as a virtual globe in the area of environmental modeling. Both make me think of the role of visualizing research results depending on the target audience and about telling the right story to the right people. I have the feeling that in my filed (geospatial information science and Digital Earth), we still miss a strong commitment to such ideas and also education has to increase on related topics. Do you share this view / maybe also in other research areas? What are your experiences?
    Roy Trevor Williams
    Hi, visualisation is essential to what we are doing, which is to try to describe the dynamics of learning in open (emergent) systems. We have developed a 3D footprint that tracks 25 variables, simultaneously, across a learning event. It could still do with some automation and interactivity, but its working for us (and for others, too).

  • Irene Baron added an answer:
    What is the future of scientific illustration?
    Hi there,

    I'd love to hear your thoughts about what you think will be the next generation scientific visualization approach. Will it be interactive? More photo-realistic? What are the skills we need to learn today to keep up in the future?

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