Archive for Training

PubMed Commons

Would you like to see a discussion by other scientists about new findings when you read a paper abstract?  Do you wish you could join in the discussion?  Do you enjoy the commentary and letters to the editor sections of journals and newspapers?  If so, read on…

 

PubMed Commons

PubMed Commons is a new service that will allow researchers to post comment on specific papers in PubMed. It is designed to be a forum that will encourage constructive criticism and high quality discussions that may enhance understanding and spark collaborations.  The screenshot below shows how the discussion displays in PubMed’s abstract view. (Click to enlarge image.)

pmcomments_example

During the time the Commons is a pilot project, participation is via invitation. If you are an author with a paper in PubMed and have eRA Commons credentials, you can invite yourself. Learn how to join PubMed Commons here.

You will need to have a My NCBI account and log into it when using PubMed.  That will allow you  to both see and post comments. To see all articles with comments on a specific topic, add AND has_user_comments[sb]  to your PubMed search.  Learn more about your My NCBI account here.

According to the NCBI, comments from the first few days after the site went live included “critique or pointed to other studies or reviews with the potential to change people’s interpretations or conclusions. Some authors posted corrections or changed their own conclusions in the light of others’ subsequent work. Authors also used PubMed Commons to update people on their work – including links to databases that have moved, providing contextual information and backstories as well as new, relevant work.

Many PubMed Commons participants took the opportunity to add links to relevant papers and data, sometimes in the non-PubMed academic literature or data repositories – including complete datasets, data re-analyses, blog posts and full text pre-prints of the article.”

PubMed Commons can be viewed as another tool in an emerging field sometimes labeled “post-publication peer-review.”  Two other options for reading commentary and adding your views to the discussion on published articles follow:

  • UAB licenses Faculty of 1000 which uses experts to identify and comment on noteworthy articles.
  • PubPeer is a free website striving to create an online community for discussion of scientific papers organized into a searchable online database.  PubPeer has released a browser plugin so users can identify articles with comments when searching PubMed.

Where PubMed Commons has requirements for the people posting commentary, PubPeer encourages anonymity.  Each has strong reasons for its requirements. If you are interested in these issues, both Nature News and Retraction Watch have discussed the PubMed Commons initiative.

NIH Research on Women’s Health

Women's Health ResourcesHave you ever searched for women’s health information and wondered whether your search results were reliable? Up to date? Complete?

Have you ever looked for research on health topics and wondered if the findings applied to women as well as men?

Women’s Health Resources is a gateway for the latest health & wellness information and sex & gender differences research. The portal is the product of a partnership between the National Library of Medicine Outreach and Special Populations Branch and the Office of Research on Women’s Health as part of the National Institutes of Health.

The Women’s Health Resources gateway can be used to improve your research and teaching activities and locate information on health topics for women.

Women’s Health Resources provides a wealth of information. Unlike other websites that may specialize in either peer-reviewed research or only consumer health information, the Women’s Health Resources portal gathers dynamically-updated peer-reviewed journal articles, clinical trials, and consumer health information into one place.

The Women’s Health Resources portal places the women’s health information into categories:

  • General
  • Alcohol, Tobacco and Substance Abuse
  • Autoimmune Diseases
  • Bone and Joint Health
  • Cancer
  • Chronic Fatigue Syndrome
  • Complementary and Alternative Medicine (CAM)
  • Diabetes
  • Exercise and Fitness
  • Heart Disease
  • HIV/AIDS
  • Lung Diseases and Disorders
  • Menopausal Hormone Therapy
  • Mental Health
  • Military and Women
  • Nutrition
  • Reproductive Health
  • Safety and Wellness
  • Sexually Transmitted Diseases (STD)
  • Violence and Abuse

The Women’s Health Resources portal also presents women’s health information based on the National Institutes of Health’s overarching themes of the priorities for research in women’s health:

  • Life Span
  • Early Years
  • Gender Identity
  • Caregiving
  • Reproductive Life
  • Senior Life
  • Health Disparities/Differences and Diversity
  • Sex/Gender Determinants
  • Interdisciplinary Research

Lister Hill Library is publicizing the Women’s Health Resources portal as part of the Women’s Health Dissemination Outreach project.  Find out more information on Women’s Health Resources by visiting the Lister Hill Library Guide or the Women’s Health Resources portal page.

Sex & Gender in Human Health

We all think about sex but how often do we think about it from an academic point of view?  How much do we know about the science and biological basis for sex/gender differences?  Do we know how these differences affect health and behavior? As students, educators, researchers, clinicians, and healthcare providers we need to understand the impact these differences have.

Get a refresher on this important information in The Science of Sex and Gender in Human Health online curriculum.

.bannerSSG

This free online series is a collaborative project presented by the Office of Research on Women’s Health, Office of the Director, National Institutes of Health; The Office of Women’s Health, U.S. Food and Drug Administration; and the Johns Hopkins University School of Medicine. Lister Hill Library received funding from the National Library of Medicine to promote Women’s Health Resources and The Science of Sex and Gender in Human Health.

The first course, The Basic Science and the Biological Basis for Sex- and Gender-Related Differences, includes the following six lessons:

  1. Understanding the Importance of Sex and Gender in Biomedical Research
  2. Legislative Process Framework
  3. Cell Physiology
  4. Developmental Biology
  5. Pharmacodynamics and Pharmacokinetics
  6. Clinical Applications of Genomics

The lessons of the second course, Sex and Gender Differences in Health and Behavior, include:

  1. Clinical Research Methodology
  2. Endocrine Effects on Immunity
  3. Drug Therapeutics during Pregnancy
  4. Understanding the Importance of Sex and Gender in Mental Health
  5. Autoimmunity, Autoimmune Disease, and Sex Bias
  6. Sex and Gender Differences in Irritable Bowel Syndrome

Each lesson can be completed in less than an hour and includes a quiz at the end to test your comprehension.  After completing each course, you are eligible for a Certificate of Completion and CME credit for physicians.

Find more information on Women’s Health Resources by visiting the LHL Guide on Women’s Health developed by SoPH Intern, Niki Agho.

WHRGUide

Trello

trello

If you’re anything like me with a hectic schedule, you’re constantly trying to find a way to keep organized and manage your physical, mental and creative space. You may use it to collaborate with team members on projects and track the stages of said project. I have good news for you; with Trello you can do just that and more.

If you’ve ever had to manage any sort of project or just try to accomplish all your personal to-do items, you know how hard it is to figure out how to track everything in a simple way, find a balanced way to prioritize all the things you have to do, and actually get them done.

Trello is awesome way to make this easier. It takes two basic steps:

First, sort your personal to-do’s into three spaces: physical, mental, and creative.

Second, use Trello.

What exactly is Trello you ask?

Trello is a free web application that you can use to track pretty much anything you want. Just go to www.trello.com and register/log in using your email address.
trello_signup

So give Trello by first:

Sorting your personal to-do items (3 spaces) physical, mental & creative.

Trello’s three main building blocks are cards, lists, and boards. Cards are things you’re working on, lists are collections of cards, and boards are collections of lists. You can put all kinds of things on the back of cards: comments, color-coded labels, checklists, file attachments, due dates, voting, and more.

One of the greatest things about this flexible (easy to use) is that you can access it on pretty much any device you choose including your pc, laptop, tablet or even smart phone. It also works with

trello_operating

Sorting your personal to-do items (3 spaces) physical, mental & creative.

Other than the 3 categories mentioned above there is also a “to-do list” as well as a “doing/waiting list” and finally the “done list”. Keep in mind you have the flexibility to edit or rename or add or delete any list as you see fit. Each item may be dragged and dropped appropriately. A great tool to use and also an alternative to the ever so popular Evernote!

Scientific Animations Without Borders (SAWBO)

SAWBOThe fact that 70% of cell phone subscribers are in the developing world has not been lost on global health innovators. A case in point is that of the creators of SAWBO, or Scientific Animations Without Borders (http://sawbo-illinois.org/main.htm), under the auspices of the University of Illinois at Urbana-Champaign. This project aims to bridge the gap between evidence-based global health interventions and those who need this knowledge the most. Unfortunately, those most in need of these interventions are often unable to access the information or understand it if they can access it due to literacy or language considerations. The SAWBO project team, in collaboration with local health, development and agricultural education agencies around the world, creates brief – about 2 minutes each – animated videos focusing on such local health issues as How to Remove Poison from Cassava Flour or Construction of a Solar Oven Using Simple Materials. These animated educational vignettes are available in multiple languages (using local accents where possible) and available for download to cell phones using Bluetooth technology. This initiative is cost-effective, scalable, and searchable using the affiliated SusDeViKi database available at http://susdeviki.illinois.edu/. Much of the work is done by volunteers, but the project receives some funding from the University, private foundations and individuals. For more information, contact the organizers at http://sawbo-illinois.org/contactus.htm.

The author wishes to thank SAWBO Director, Dr. Barry Pittendrigh, for his input for this blog entry.

Much Ado About MOOCs

The term MOOC was coined in 2008 but over the past year, MOOCs have become all the rage. So what are MOOCs and why all the hype?

What is a MOOC?

In the simplest terms, MOOCs are Massive Open Online Courses. University faculty from leading universities (Harvard, MIT, Yale, McGill, Australian National, etc.) around the world teach MOOCs and they are open to anyone with Internet access. MOOCs have a start date and an end date similar to a real in-person class. Some have weekly assignments, tests for comprehension, and offer credit or certificates for completion. I should mention there are different opinions of what truly constitutes a MOOC among the MOOC-faithful so here is a video from one of the MOOC concept creators, David Cormier:

If you want to read about the different type of MOOCs (xMOOCs and cMOOCs), see this blog post.

MOOCs offer instruction from a wide range of disciplines including Computer Science, Engineering, Business, Humanities, Science, Mathematics, and Health & Medicine. Here are some specific examples of course topics:

Here is a Ted Video clip featuring Peter Norvig on his MOOC teaching experience: The 100,000-student classroom.

How do I find one?

You can go directly to some of the providers such as edX, Coursera, Udacity, or you can use a MOOC aggregator like Class Central.

Challenges for MOOCs

I would be remiss if I did not make at least a passing mention of some of the challenges for MOOCs. MOOCs are still very new, experimental, and prone to failure. Educators are still trying to find ways to measure success and effectiveness of MOOCs. The attrition rate for MOOCs has garnered some negative attention with some examples citing that as little as 10-15% of enrolled students actually completing a class. MOOCs are a different type of educational tool so applying traditional metrics DOES NOT make sense. The question is what metrics should be applied to determine success or failure of a course; or more broadly, the MOOC concept?

My two cents

The jury is still out on whether MOOCs are an effective education tool, but I think it depends on why YOU decide to register for a MOOC. If your goal is to get exposure to a topic of interest, continue education, or just examine course content, I think it is a worthwhile tool with minimal investment. If you are looking to get college credit, I would encourage take a critical look at partnerships such as MOOC2Degree.

Tell Me Your Story… But Make it Fast!

Everyone has a story to tell. But telling a story in a concise manner is difficult for many of us. Some of us tend to ramble and eventually get to the point but maybe lose some of our audience in the process.

In 2006, Brady Forrest from O’Reilly Media and Bre Pettis from Makerbot.com, formerly of MAKE Magazine, hosted an event called Ignite to help presenters share their personal and professional passions. The “geek event” was meant to bring together people from a community to “ignite” awareness and thought on the subjects presented. The format was successful and has been used in cities all over the world.

Ignite format talks are a style of presenting where people speak on a subject of their choice for five minutes accompanied by 20 PowerPoint slides. The slides are automatically advanced every 15 seconds. At the end of five minutes, the Ignite talk is over!

Here is an Ignite presentation from O’Reilly author Scott Berkun on “How and Why to Give an Ignite Talk”

Talks in this format could be a great benefit in the classroom, clinic, or lab. In the classroom, Ignite can serve as a teaching and learning tool for students to talk about projects in a structured format. Clinicians naturally have to be brief in the practice setting. Training residents and trainees to adopt a concise presentation format for case presentation will benefit them later in their careers. Researchers can also benefit from using this format to discuss their latest findings and identify potential collaborators. The Ignite format can be intimidating, but with a little bit of practice you will be golden. Stay tuned for some teaching sessions on How to Give an Ignite presentation or contact Gabe at grios-at-uab-dot-edu. Here are some resources to help you put together your first Ignite presentation:

I have personally attended Ignite events at my national professional conferences and we had the privilege of co-hosting the very first Ignite Birmingham here at the Lister Hill Library in 2010. The Lister Hill Library is collaborating with the Edge of Chaos and Ignite Birmingham to host an Ignite event here in the Edge of Chaos (the fourth floor of the Lister Hill Library) on September 20, 2012. Check out the Ignite Birmingham webpage for more information about this event and videos of past events. Dust off your PowerPoint skills and get ready to IGNITE others with your passions!

Raspberry Pi, Anyone?

Want to buy a computer for $35?  Look no further than the Raspberry Pi.  No, I’m not a salesperson for the the Raspberry Pi.  It’s is a credit card-sized computer created by Cambridge University educators in the UK to provide an affordable platform for children to gain computer programming skills.  What does that have to do with me?  Not a lot. As someone who likes technology but doesn’t consider herself a “techie” (especially when it comes to hardware and operating systems), I thought it would be fun to experiment with at such an affordable price.

When I first learned about the RPi, I was put on a waiting list because of the high demand for the little sucker.  Once I paid for it, it still took about six weeks to arrive.  So if you’re in a hurry, the RPi is not for you.  Be aware that the RPi will need standard computer accessories, such as cables, power, mouse, keyboard etc.  It looks like this:

As you can see, it comes without a case.  This is something I didn’t consider when I ordered mine. There are a few DIY case-making options in the Raspberry Pi discussion archives.  I elected to order a case and am waiting for it to be back in stock. In the meantime, I’m storing it in the box it came in when not in use.

To get the RPi up and running, you will also need and SD card loaded with an operating system.  I ordered one pre-loaded from them directly, but you can buy your own and download the Linux OS here for free.  I hooked my RPi up to my television using an HDMI cable. So far, I’ve only surfed the web a bit with it, but the potential applications are numerous, including standard word processing, spreadsheets, games, and programming.  To get started, check out RPi Beginners Wiki. PC Magazine has a review of RPi here.

Does this sound interesting to anyone else?  I may post a follow-up once I’ve had a chance to get to know my RPi better.

Learning to be a Web Geek

So you want to learn to do web development stuff but don’t have access to real web server. No problem! All the programs you need to create a web server are available free. There are even tools that will install the programs you need in one package. Two of the most popular are WAMP and XAMPP.  I’m a Windows person so I’m going to be referring to Windows installs but you can get versions of these kinds of packages for just about any OS.

First, let’s look at WAMP, which stands for Windows, Apache, MySQL, and PHP. Installing WAMP couldn’t be easier. Just point your browser to http://www.wampserver.com/en/ and scroll down to the download section and download the version you need for your OS. The first thing you will see is the Welcome to the WampServer setup. This box tells you the software and versions you will be installing.

WAMP Install Screen

Once installed you get a nifty little control panel for your system tray. Here you can configure everything you need to run your development environment.

WAMP Task Bar

XAMPP works much the same way. On their home page http://www.apachefriends.org/en/xampp.html download the version for your OS and you are off and running.  Watch out for their site though.  The top of the screen has a big download button and you don’t want that. You want to scroll down until you see Download XAMPP and it jumps you down a bit and you want to pick the link that says installer.

XAMPP Install Screen

You get a control panel for XAMPP too.

XAMPP Control Panel

The main difference in the two other than interface is that XAMPP includes Perl so if you need Perl go with XAMPP otherwise I am not sure it matters which you choose.

Basically once you have one of these installed you can start playing with things like Joomla!, Drupal, or other software that runs on LAMP on your local machine. Open a web browser and type in http://localhost to see what you’ve done. Here is a WAMP example:

WAMP Localhost.

 

It is an easy way to learn without having to pay for web space or fear of embarrassing yourself!

Caveats: While both installers are released under GNU always take a look at the licenses for each piece of the install. The PHP license may be a little different than the Apache license. You just want to make sure you aren’t breaking any rules. Second, the default settings aren’t always the best option or the configuration that will work with what you are trying to do. Make sure you take the time to configure everything properly. Third, double check what versions are being installed with what program you want to install. In other words make sure the programs you are installing with WAMP/XAMPP match the versions needed by Joomla, Drupal, etc. Fourth, if you actually plan to upload what you create to another web server make sure the program version you have on your machine match what is on the web server you are transferring those file to.

Learning to Program is Cool Even if I’m No Good at It

Being in IT I’ve always felt like I should be able to program at least a little. I’ve come to realize that ‘programming a very little’ is most likely as good as I will get. After all I did choose my undergraduate school based on my ability to engineer my degree so as to take absolutely NO MATH. But with that said knowing about programming has helped me immensely in my job and with technology in general. If you are interested in learning to program or just learning about how programming works there is a regular cornucopia of free stuff to help you.

One of my absolutely favorite resources is Harvard Professor David J. Malan’s Introduction to Computer Science I. This course is for non-computer science majors as well as the students that have already declared computer science.  First, the guy is a fantastic instructor and speaker. Second, you have access to everything the actual student experienced. It is like taking the course yourself. The course is a great broad overview of computer science and programming.  Take a look at This is CS 50 which appears to be updated for Fall 2011.

If you work at UAB there are a number of really good programming courses offered by Training & Development .  But even if you can’t take the courses there are still tons of things online. For instance, the Programming Basics classes uses Java and materials from Central Connecticut State University Professor Bradely Kjell’ Introduction to Computer Science using Java website. You can go through the chapters, quizzes and exercises on this site to get some experience.

If you are into web development stuff w3schools is one of the best resources out there. These free tutorials cover a multitude of topics as well as quizzes and they even have a certificate program.

But don’t stop there. You can download just about any programming environment you want. For the Programming Basics we used Netbeans. It was super easy to install and use. The screenshot below is from my Netbeans install with the little programs we used in the class. The actual Java Tutorials are pretty good too.

But if you aren’t going to actually program for money why bother you ask? Well, for me at least it does several things. One of the most important things it does is help me communicate with real programmers better and gives me a much broader understanding of IT in general. I also supervise someone that does some programming so it helps me help him and understand his work better. It also really makes me use my brain in ways that I don’t usually. I have to really work at it and using your brain especially as you age has all sorts of positive benefits. Meeting new people that may actually become programmers is another benefit.  Another really important thing for me is I can’t write code from scratch but I can read it and I can fix written code a good bit of the time too.

But it is scary to go into something you know nothing about and you are afraid you will feel silly or embarrassed you say? Well my first bit of advice is to get over that right now. Let yourself be ok with knowing nothing and learning at your own pace.  Some other advice includes picking a language and sticking with it until you are very comfortable with that one language. At one point I had picked introductory books on four different languages. This wasn’t good for my sanity or frustration level. Pick something you like and run with it. Once you get the fundamentals and basics down you can more easily learn another language.  If you have ever wondered how programming works or if you have a knack for it there is absolutely no excuse for not checking out these resources or any of the thousands of others.