Jump to student posts!

Our goal in this section of the workshop is to introduce you to several categories of tools that every graduate students should know about. We will focus on one tool in each category but there are many other options that you may find work better or others in your lab are using.  Plus, it is the nature of these tools being on line that they are changing all the time.  So we will focus more on the big reasons for using these tools less on the particulars of any specific tool.

Overview: As we introduce each category of tool you will get some hands on experience using it. To make this as useful as possible we suggest that you work in a research area that is important to you. You will be creating accounts for each tool, saving some data, and sharing it with the group.

Bibliographic Management Tool – Mendeley [http://www.mendeley.com/]

Mendeley is a free reference manager and academic social network that can help you organize your research, collaborate with others online, and discover the latest research. Mendeley is a combination of a desktop application and a website which helps you manage, share and discover both content and contacts in research. For more information see – Mendeley FAQ – [link]

Assignment: Sign-up for a Mendeley account and “collect” a few papers that are in your research area. You might want to install the desktop software and the web importer. You can also join the Peer 2012 Shared Papers group [link]

Other tools in this category

Online Research and Social Bookmarking Tool – Diigo [http://diigo.com/]

Diigo aims to dramatically improve your online productivity.   Building upon the strengths of award-winning Diigo V4, widely regarded as one of the best and most popular social bookmarking, web annotation, collaborative research services,  Diigo V5.0 has added additional data types (screenshots, pictures, notes, etc) and platform support, such as Chrome, Android, iPad, iPhone, etc.  With Version 5.0, Diigo moves one step further towards its vision of providing the best cloud-based  personal information management (PIM) service that enables users to collect, highlight, access and share a variety of information, on a variety of devices. For more info see [http://help.diigo.com/].

Assignment: Sign-up for a Diigo account and “collect” some web based resources that are in your research area. You might want to install the bookmarklet to make it easy to add and annotate items for your collection. You can also join the Peer 2011 Diigo group [http://groups.diigo.com/group/peer-2012]

Other tools in this category

RSS Reader – Google Reader [http://reader.google.com/]

Have trouble keeping up with the sites you visit? Read them in one place with Google Reader, where keeping up with your favorite websites is as easy as checking your email. Stay up to date: Google Reader constantly checks your favorite news sites and blogs for new content. Share with your friends: Use Google Reader’s built-in public page to easily share interesting items with your friends and family. Use it anywhere, for free: Google Reader is totally free and works in most modern browsers, without any software to install.

RSS in Plain English [http://www.youtube.com/watch?v=0klgLsSxGsU]

Assignment: Sign-up for a Google Reader account and subscribe to some feeds. Be sure to include some custom feeds (see options below) in your research area.  You can see my public feeds page here – Sam’s Public RSS Page on Google Reader – [link].


NCBI/PubMed [http://www.nlm.nih.gov/bsd/disted/pubmedtutorial/040_060.html] Part of the “PubMed Tutorial”, the Web-based learning program that will show you how to search PubMed®, the National Library of Medicine (NLM®) journal literature search system.

Blogs [http://technorati.com/] The leading blog search engine, Technorati.com indexes millions of blog posts in real time and surfaces them in seconds.

Google Alerts [http://www.google.com/alerts] Google Alerts are email updates of the latest relevant Google results (web, news, etc.) based on your choice of query or topic.

Journals and popular science outlets – just a few examples

Science [http://www.sciencemag.org/rss/]

Nature [http://www.nature.com/nature/newsfeeds.html]

New York Times Science Section [http://www.nytimes.com/services/xml/rss/index.html]

Science News [http://www.sciencenews.org/view/page/id/45/title/syndication]

Make a blog posting to the PEER 2012 Workshop page [http://bioquest.org/peer2012/]

Blogs in Plain English [http://www.youtube.com/watch?v=NN2I1pWXjXI]

Final Assignment (for now): Login to WordPress [http://bioquest.org/peer2012/wp-login.php], Create a new post and share: [http://bioquest.org/peer2012/wp-admin/post-new.php] with the following information.

  • Introduce yourself (professional only)
  • Statement of research area you built your “collaborative online information tracking system” around, and
  • Links to the resources you created using Mendeley, Diigo and Google Reader (see below).

A bit more information about what and how to share your collections in your blog posting.

Mendeley: Ok, so I thought that it was easy to share your collections (folders) but the software has changed. You can only share groups (make them visible to users who are not logged in). See the FAQ [link] for more information. So, you can just include a link to the Peer 2012 group (where I assume you have shared your paper collection) in your blog post.

Diigo: This one is pretty straight forward. If you have made any bookmarks and annotations public they should appear on your public page. Here is the format for the link [http://www.diigo.com/profile/samdonovan] – just change the username and you are set to share it in your blog post.

Google Reader: There are lots of options here. To share selected items from any of your feeds click the “share” link at the bottom of an entry. Then they will appear on your public page [http://www.google.com/reader/shared/ssdonova] – again, just change the username for your address. You can also share folders (a folder contains one or more feeds). You assign feeds to folders and set the public status of folders when you follow the “manage subscriptions” link – found at the bottom of your list of subscriptions. Here is an example of a folder I’m sharing called cyberlearning lab that collects several feeds I follow. You should include a link to some shared reader info in your blog post.

Just ask if you have questions or need a hand with this.

Posts about us:

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