Digital tools for researchers
2.7K views | +0 today
Follow
Digital tools for researchers
Digital tools for researchers (science 2.0): research, lab and data management, publication & citation management, collaborative working, data visualization, virtual teams,
Your new post is loading...
Your new post is loading...
Scooped by Tree of Science
Scoop.it!

The value of archive content in academic research Research Information

The value of archive content in academic research Research Information | Digital tools for researchers | Scoop.it

Is archive content relevant to current research and why is it still so valued in the ‘digital era’?



Tree of Science's insight:

‘Archive content’ can simply be defined as artefacts from the past. This content appears in many forms, such as documents, photographs and recordings, all of which represent former discoveries and offer a background to past research findings. Often a reliable source of primary research, archive content documents significant historical findings, providing a level of accountability to current research. In this digital age, why is older research still valuable in university teaching and relevant to present-day research? #archive #digitaltoolsforresearch #science2dot0

more...
No comment yet.
Scooped by Tree of Science
Scoop.it!

Mahotas: Open source software for scriptable computer vision

Mahotas: Open source software for scriptable computer vision | Digital tools for researchers | Scoop.it

Mahotas is a computer vision library for Python. It contains traditional image processing functionality such as filtering and morphological operations as well as more modern computer vision functions for feature computation, including interest point detection and local descriptors. (...) - Journal of Open Research Software, par Luis Coelho, 29/07/2015

more...
No comment yet.
Scooped by Tree of Science
Scoop.it!

It’s ok to be lazy with the Google Scholar Button

It’s ok to be lazy with the Google Scholar Button | Digital tools for researchers | Scoop.it

Google comes with a new serviceable solution for researchers. The Google Scholar Button has become a hit in the past few weeks. It also almost made me cry with joy. What is so useful about it?

 

The Google Scholar Button extension is currently available for both Chrome and Firefox browsers, which means for the majority of Internet users. The add-on has already been installed by more than 374 thousand Chrome users and 27 thousand Firefox users (there are plenty of scholars around the world, right? (...) - Open Science, May 22, 2015

more...
No comment yet.
Scooped by Tree of Science
Scoop.it!

Visual Pubmed

Visual Pubmed | Digital tools for researchers | Scoop.it

Visual Pubmed. Scientic literature search revisited, Medline, Citations, Impact Factor

Tree of Science's insight:

By Raul Catena: "It really changes the way you can explore scientific publications in the Biomedicine field"

more...
No comment yet.
Scooped by Tree of Science
Scoop.it!

Repository Highlight: figshare and the crucial service of generalist repositories

Repository Highlight: figshare and the crucial service of generalist repositories | Digital tools for researchers | Scoop.it

Scientific Data works with over 60 public data repositories and helps authors find the best place to store their data. We require authors to store their data in community-recognized data-type-specific repositories when they exist. But for many data-types, specific repositories do not exist. In these cases, broad repositories, such as figshare, that can host a wide range of data-types provide a crucial service to the scientific community. (...) - by Andrew Hufton, Nature, March 8 2015

Tree of Science's insight:

Share datasets in repositories provide to researchers a way for more transparency about their data used in published (or future) articles. This improves #reproducibility in scientific #research, which represent now a critical issue in research field. Repositories offers mainly DOIs in order to secure the datasets. #openresearch

more...
No comment yet.
Scooped by Tree of Science
Scoop.it!

labfolder upgrade and new features

labfolder upgrade and new features | Digital tools for researchers | Scoop.it

As part of the latest labfolder upgrade, the electronic lab notebook now comes with a new design and research tools to improve workflow management processes. (...) - by Simon Bungers, labfolder blog, January 15th, 2015

Tree of Science's insight:

The free digital notebook to organize research (protocol and data management, collaborative features...) has release a new version this year. They greatly improve user experience and design by improving the research workflow: the sidebar goes to a top navigation bar; the interface has now a facebook-like timeline called "Research Chronology", and new entry titles bring a nice overview on files and projects shared. 
Other features have been added: a filter-function inside the notebook, tags on research files, customs dates, and a useful to-do list. 

more...
No comment yet.
Scooped by Tree of Science
Scoop.it!

CrossRef and DataCite announce new initiative to accelerate the adoption of DOIs for data publication and citation

DataCite and CrossRef have agreed to collaborate to:

- Enhance the interoperability of their respective systems in order to make it easier for publishers, data centres, libraries and third parties to integrate with the scholarly DOI ecosystem.

- Provide comprehensive support for interlinking between articles and data.

- Develop open APIs and open source tools to surface citations and other relationships between publications and data sets. 

- Integrate into their services other existing scholarly communications initiatives such as ORCID and CrossRef’s FundRef.

- Develop systems, workflows and best practices for using DOIs to reference large, highly granular and dynamic data. 

(10 November 2014, Oxford, UK)

Tree of Science's insight:

With the huge increase of data in scientific research (+30% every year), the data management becomes now a critical issue and implies also more links of publications to their data. Moreover the community of researchers is going more and more in the open research process to open data and thus improve their reuse (reproducibility), citations, and sharing. 


In this area, DataCite and CrossRef manage around 75 millions DOIs that identify research objects. In order to accelerate their growth with the adoption of DOIs for data publication and citation, they decide to collaborate and improve their interoperability. Other platforms for researchers integrate DOIs:  for data management like Figshare (1 millions) and for scientific blogging like The Winnover.

more...
No comment yet.
Scooped by Tree of Science
Scoop.it!

The "Paper" of the Future | Authorea

A variety of research on human cognition demonstrates that humans learn and communicate best when more than one processing system (e.g. visual, auditory, touch) is used. And, related research also shows that, no matter how technical the material, most humans also retain and process information best when they can put a narrative "story" to it. So, when considering the future of scholarly communication, we should be careful not to do blithely away with the linear narrative format that articles and books have followed for centuries: instead, we should enrich it. (...) - by Alyssa Goodman et al., Authorea

Tree of Science's insight:

Research articles exclusively published on paper has been progressively replaced in a main part by pdf files and online readings. This paper written on the collaborative platform for scientific articles writing, Authorea, deals about the new generation of articles in scientific research related to a "article 3.0" integrating all forms of graphics, tables,videos, collaborative post-publication #review, annotations, meta-data, ... 

You will also find a useful table comparing the different online platforms that provide collaborative writing opportunities. 

more...
No comment yet.
Scooped by Tree of Science
Scoop.it!

Arkivum and figshare announce partnership

Arkivum and figshare announce partnership | Digital tools for researchers | Scoop.it

Arkivum and figshare have joined forces to provide a solution covering the full spectrum of funder-mandated research data requirements.

 

Arkivum, the provider of large scale, long term, and ultra-safe digital archiving solutions and figshare, the research data management platform that specialises in ‘active data’, have announced a partnership to provide a solution covering the full spectrum of funder-mandated research data requirements for UK academic institutions. (...) - arkivum blog, 9 September 2014

Tree of Science's insight:

Figshare manage to offer more safe and long-term digital archiving solution by establishing a partnership with the UK company Arkivum .

 

Image courtesy of renjith krishnan (FreeDigitalPhotos.net)

more...
Julien Hering, PhD's curator insight, March 4, 2015 8:33 AM

New improvement for Figshare, the collaborative data management platform: partnership 

Scooped by Tree of Science
Scoop.it!

Digital Science invests in WriteLaTeX

Digital Science invests in WriteLaTeX | Digital tools for researchers | Scoop.it

We're delighted to announce that WriteLaTeX has secured investment from Digital Science to support the continued development of our collaborative science platform, Overleaf.

If you've not yet tried it, Overleaf is our easy-to-use WYSIWYG manuscript editor with real-time collaboration that produces structured, fully typeset output automatically as you type. It’s a great way to start developing your scientific manuscript, especially one with multiple authors/contributors.  (...) - writeLaTeX Blog, July 23, 2014

Tree of Science's insight:

After buying Labguru (research management platform) and figshare, the british Digital Science company (a division of Macmillan Science & Education) is now continuing its growth by investing in WriteLaTeX. 

more...
No comment yet.
Scooped by Tree of Science
Scoop.it!

PubMed Update: Social Media Icons Added

PubMed Update: Social Media Icons Added | Digital tools for researchers | Scoop.it

The PubMed Abstracts now display social media icons for Facebook, Twitter, and Google+. - NLM Technical Bulletin. 2014 Jul–Aug

Tree of Science's insight:
PubMed is one of biggest citations databases for biomedical literature with more than 22 million citations from MEDLINE, life science journals, and online books. You have now the opportunity to directly share abstracts to social media (#facebook, #twitter, #google+) from PubMed.
more...
Scooped by Tree of Science
Scoop.it!

Zotero awarded to improve several new features

Zotero awarded to improve several new features | Digital tools for researchers | Scoop.it

Zotero has been recently awarded by two foundations to develop and asses new functionality in collaboration with several universities.

 

The Andrew W. Mellon Foundation has funded a two-year collaboration between Penn State and George Mason University to develop and assess new Zotero functionality. At first, RSS and Atom feeds that enable users to follow scholarly journals and easily collect publications by simply dragging them to their Zotero libraries. Moreover Zotero will turn into a institutional repository (IR) for at the beginning Pen State university students and staff to deposit self-authored works directly into the IR from Zotero. A pluggable architecture will then be also developed to enable other IR to establish similar connections with Zotero. Like an iFTT for Zotero, a push-based API and a standalone service that connects Zotero to other third-party web applications.


The Alfred P. Sloan Foundation has funded Zotero and two other universities to develop a preliminary API that returns anonymous readership counts when fed universal identifiers (e.g. ISBN, DOI), enabling bibliometric research and integration into third-party apps. The research will help to improve our understanding of social media’s value in scholarly communication and the actual meaning of various altmetric scoring systems.

more...
No comment yet.
Scooped by Tree of Science
Scoop.it!

How to get indexed by Google Scholar?

How to get indexed by Google Scholar? | Digital tools for researchers | Scoop.it

Google Scholar is an 'invitation based search engine’, which means it index content cited by articles already indexed are included in the database. (...) - Blog Open Science, April 11, 2014

Tree of Science's insight:

Researchers are using different ways to find scientific articles for their work : free field-centered search engines (i.e. PubMed for life science) or services with subscriptions (like EBSCO, ProQuest, ...). Google Scholar is one of the most worlwide used. To be easily founded, researchers have to correctly indexed their articles. #research #science2dot0 #scientificpublications

more...
No comment yet.
Scooped by Tree of Science
Scoop.it!

Hybrid Lecture Player – McLuhan Archives. Prototype launch

The Hybrid Lecture Player is a new open source platform release that allows you to turn lecture documentation into a multi-format publication. (...) - Hybrid Publishing Lab, by Simon Worthington, July 3, 2015

Tree of Science's insight:

The Hybrid Lecture Player is a platform that allows you to turn your lecture documentation into a multi-format publication, with a toolkit with features such as subtitle transcription, transcription in prose form, translations, and embedded lecture material such as images, audio and visual files. #science2dot0 #digitaltoolsforresearchers

more...
No comment yet.
Scooped by Tree of Science
Scoop.it!

Push, Pull, Fork: GitHub for Academics

Push, Pull, Fork: GitHub for Academics | Digital tools for researchers | Scoop.it

In his article, “Open-source Scholarship”, Kris Shaffer argues that the open-source software model has lessons to offer the academic community. Here, Kris demonstrates how a scholar can put open-source philosophy into practice using a specific tool developed by and for the community: GitHub. (....) - Hybrid Pedagogy, by Kris Shaffer, May 26, 2013

Tree of Science's insight:

GitHub is an amazing resource designed for collaboration on open-licensed projects with text, code sharing, open-source... consistent with the ideology of open research. You may even use Github to host a non-standard form of website as Kriss descried it or use it as GitXiv to create a collaborative platform in the field of computer science #science2dot0 #openscience

more...
No comment yet.
Scooped by Tree of Science
Scoop.it!

SAGE Video

SAGE Video | Digital tools for researchers | Scoop.it

SAGE Video, streaming video collections in the social sciences, created for use across higher education. SAGE Video combines originally commissioned material with licensed videos in the areas of Education, Media, Communication and Cultural Studies, and Counseling & Psychotherapy 

Tree of Science's insight:

Sage has launched Sage Video a streaming video collections to support a large range of needs across higher education and higher-level academic study and research.


The first three collections of video content already available include education, communication and media studies, and counselling and psychotherapy. More collections will be added in 2016. 'Sage Video represents an important next step in our 50-year journey as a social and behavioral science publisher,' said Stephen Barr, president of Sage International. 'The video collections were designed after conducting robust research about changing student needs, instructor preferences, and library support of the research-and-learning ecosystem.  'We are confident that these new video resources will enrich the research and learning experience in a unique way by intimately connecting learners to experts in social science fields, truly bringing teaching, learning, and research to life.'


The videos collections were created by taking each discipline and mapping key topic areas to video briefs. Each collection has had oversight from international editorial boards, including Sage authors and editors, and academic partners.

more...
No comment yet.
Scooped by Tree of Science
Scoop.it!

Data visualization: Science on the map

Data visualization: Science on the map | Digital tools for researchers | Scoop.it

Easy-to-use mapping tools give researchers the power to create beautiful visualizations of geographic data. (...) - Nature, by Mark Zastrow, 04 March 2015

Tree of Science's insight:

Data visualization is a critical issue in science and science communication. Several digital tools help researchers to create #dataviz for greographic datasets #scicom

more...
Enrico De Angelis's curator insight, December 26, 2015 2:47 AM

DONT BE AFRAID OF DATA ANALYSIS TASKS

"Even researchers who would rather not touch a line of code can accomplish a lot with the help of CartoDB and TileMill. “You don't have to be particularly technically competent,” says Gawne, who produced the Tibetan-language maps for her thesis in TileMill and now teaches mapping workshops herself!.

Scooped by Tree of Science
Scoop.it!

Programming: Pick up Python

Programming: Pick up Python | Digital tools for researchers | Scoop.it

A powerful programming language with huge community support.

 

Last month, Adina Howe took up a post at Iowa State University in Ames. Officially, she is an assistant professor of agricultural and biosystems engineering. But she works not in the greenhouse, but in front of a keyboard. Howe is a programmer, and a key part of her job is as a 'data professor' — developing curricula to teach the next generation of graduates about the mechanics and importance of scientific programming. (...) - by Jeffrey M. Perkel, Nature, 04 February 2015

Tree of Science's insight:

Researchers of every disciplines from biochemistry to humanities are using more and more coding to help them data analysis, data management, data gathering... These scientific programmers often choose now Python language for programming according to its accessibility to learn and the collaborative communities. They routinely use a small set of Python core and software packages according to their field or needs in their workflow:

 

- In modelisation: PyDSTool and simulationSimPy.

- In mathematic: with NumPy (mathematical arrays), SymPy (symbolic mathematics), APM Python, PyGTS (3D surfaces), sspy, mpmath, clnum, uncertainties, soerp

SciPy, FuncDesigner, OpenOpt, SpaceFuncs, !Nlopt, escript, PyIMSL (scientific algorithms library)

- In GIS, mapping, Image Processing and Analysis: Thuban, PySAL, Python Cartographic Library, OWSLib, GeoJSON, and Rtree, sDNA

- In #machinelearning with scikit-Learn, mlpy

- In bioinformatics with Biopython, PyCogent (COmparative GENomic Toolkit), track (read/write access to genomic tracks), PyChem, bx-python, p4 (phylogenetics), UCSF Chimera PyMol (3D molecular viewer)

- In psychology and neuroscience with PsychoPy and PyLink (eye tracking)

- In Space Science Astropy SunPy SpacePy

- In Physics with Astropy (Astronomy), QuTip (quantum mechanics), ObsPy (seismology)

more...
No comment yet.
Scooped by Tree of Science
Scoop.it!

SciRev - Review the scientific peer-review process

SciRev - Review the scientific peer-review process | Digital tools for researchers | Scoop.it

The SciRev platform offers to researchers the possibility to publish reviews about their experience with the peer-review process of specific journals. The following topics are discussed: the duration of the first review round, the total handling time, the number of reviewers, the quality of the reviews, personal experience with the journal, and an overall rating of the process. SciRev also allows you to compare several journal side by side.

Tree of Science's insight:

The peer-review processes of research articles is for a while now under the eyes of researchers to improve this critical process in their workflow. SciRev helps researchers to choose the right journals to publish in and also to improve the publishing system by the rating system. Combined with a platform like JournalGuide, the journal-rating platforms could become keypoint to identifying the journals that are ahead of the peer-review game. 

more...
No comment yet.
Scooped by Tree of Science
Scoop.it!

Google Scholar pioneer on search engine’s future

Google Scholar pioneer on search engine’s future | Digital tools for researchers | Scoop.it

As the search engine approaches its 10th birthday, Nature speaks to the co-creator of Google Scholar. (...) - Nature, by Richard Van Noorden, 07 November 2014

Tree of Science's insight:

From the idea of improving the ranking of scholarly documents to a powerful search engine dedicated to scholarly items (more than 100 million), Google Scholar succeed to reach almost 2/3 of scientists. Author profile pages and a recommendations engine have also been added since 2012 #research #researcharticles 

more...
No comment yet.
Scooped by Tree of Science
Scoop.it!

Anonymous peer-review comments may spark legal battle

Anonymous peer-review comments may spark legal battle | Digital tools for researchers | Scoop.it
legal battle embroiling PubPeer, an online forum launched in October 2012 for anonymous, postpublication peer review
Tree of Science's insight:

PubPeer is an anonymous postpublication peer review platform launched in October 2012. PubPeer has recently entered in a legal battle linked to defamation about several comments that tends to insinuate deliberate misconduct in research. To answer the requests of the identity of the commenters, PubPeer has argued that researchers should defend their papers against online comments without resorting to legal action. PubPeer’s moderators has already remove some because in violation of their posting guidelines. The question remains about the reliability of anonymous postpublication peer review process for research papers. 





more...
No comment yet.
Scooped by Tree of Science
Scoop.it!

How 'Google Science' could transform academic publishing (Wired UK)

How 'Google Science' could transform academic publishing (Wired UK) | Digital tools for researchers | Scoop.it

Google is allegedly working on a free, open access platform for the research, collaboration and publishing of peer-reviewed scientific journals. (...) - by Liat Clark, Wired UK, 13 August 2014

Tree of Science's insight:

Google Science project is mostly build around all the Google tools already existing for editing, share and collaborate (Google docs, sheets, drive...). The community of researchers will self-managed and based and Google+. Journals would be able to be created by members themselves and peer-reviewed by scientists of the communities. Google analytics will be used as altmetrics of published articles.

Will it works with a platform based on "ten percent tools and technology, and 90 percent community? A Self-governing community of researchers would be able to generate an active life on the platform?

more...
Hazman Aziz's curator insight, November 9, 2014 10:18 AM

Google might able to change this. Previously, we have Google Knol. 

Scooped by Tree of Science
Scoop.it!

Startup of the Week: Figshare (Wired UK)

Startup of the Week: Figshare (Wired UK) | Digital tools for researchers | Scoop.it

Figshare wants to open up scientific research and data to the world. The idea was first born in 2010 while founder Mark Hahnel was studying at Imperial College London, before a 2012 launch. He wanted to develop a way to share all kinds of datasets -- digital and otherwise -- in an easy-to-use, opensource way. At that point it was just to "allow scientists and researchers like me to get credit and recognition for all their work," says Hahnel. Two years on and the platform now has employees in the UK, US and Romania and serves hundreds of thousands of researchers a month, hosting more than 1.5 million files.  (...) - Wired UK, 25 July 2014

more...
No comment yet.
Scooped by Tree of Science
Scoop.it!

Extracting data from plots, images, and maps with WebPlotDigitizer

Extracting data from plots, images, and maps with WebPlotDigitizer | Digital tools for researchers | Scoop.it

It is hard to understand why in today’s all-interactive world, scientific data continues to be represented as still, lifeless images. Sadly, the good old pdf or html versions of research papers do not allow us to extract and reuse the data represented as graphics. While we wait for publishers to finally bring interactive figures to publications, and for data to be more open an easily accessible, a simple and reliable method to extract data from graph would be great. Lucky for us,WebPlotDigitizer does exactly that! (...) - Blog "Connected Researchers", June 12, 2014

more...
No comment yet.
Scooped by Tree of Science
Scoop.it!

Will Digital Humanities #Disrupt the University?

Will Digital Humanities #Disrupt the University? | Digital tools for researchers | Scoop.it

It’s no secret that the humanities—literature, history, philosophy, the foreign languages— are suffering from a precipitous plummet in higher education. But hark! Digital humanities are here to rescue the field—or maybe just kill it off for good. (...) - by Rebecca Schuman, Slate, April 16, 2014

Tree of Science's insight:

Digital humanists are using  digital tools for researchers and are more often practicing  open science. But is it good at least that they tend to become like computer scientists? 

more...
No comment yet.