Week 5: Project-based learning resources

pbworks (one of many wiki platforms)


pbworks is only one of many free wiki services offered on the internet. Those who teach using Moodle have the chance to use the wiki tool built right into the program. Wikis are an amazing way to keep track of student participation and learning during a project. Sandra Porter’s post on her blog Discovering Biology in a DIGITAL WORLD highlights the ways she uses wikis in her bioinformatics class: she posts her syllabus, lab activities, assessment questions, and has pages for student notes. Since this is a collaborative resource, it satisfies NETS-T 1 (c) and NETS-T 5 (a). Specifically, wikis provide an excellent way for students to share their creative process and notes, and sharing can also be done between local teachers or those from around the world to further help their students.


Poll Everywhere


I have used this online polling service before to assess my students’ perception of a topic before getting into it. With this tool, students are able to respond to prompts in real time via texting. A poll would be a good addition to any learning project for assessing student knowledge before, during, and after the project. The relevant NETS for this tool are: NETS-T 2 (a), since the site uses cellphones, a new digital resource, to promote learning. Also, NETS-T 3 (d) is reached by using a current digital resource to gather data from the students, helping to evaluate their learning needs.


Case Collection –  National Center for Case Study Teaching in Science at the University at Buffalo


Case study use in science education can help teachers convey scientific content as students develop their critical thinking skills. The projects included in this page involve contemporary issues that anyone can find in the news. The website includes basic information about each project (abstract, keywords, objectives), teaching notes, and the case study itself in a pdf file that is so thorough it could go straight from the website into the classroom. This perfectly exemplifies NETS-T 1 (b), as the case studies are from real world issues, and students can use them to develop their problem solving skills and critical thinking. Case studies are also related to NETS-T 2 (b), as the case studies could be chosen by each student, and studied and answered at their own pace.


Microbe World Video


These video podcasts by the American Society for Microbiology highlight the most interesting aspects of Microbiology and the most critical medical news- such as flu outbreaks, the use of microorganisms to make biofuels, vaccine efficacy, etc. These would be great introductions to learning projects. The podcasts here fit with NETS-T 3 (c) by properly communicating important information to the students on the processes involved with Microbiology, but also on career information and the tools of the trade. NETS-T 5 (c) is also covered since the collection of videos covers current practices in the field.


Internet for Microbiology


This is an amazing guide that teaches students to use the internet like a Microbiologist- it talks to them about the process of academic research, finding sources, evaluating them, publishing, communication, etc. and how to use current digital resources to accomplish this. It comes with a huge list of all kinds of resources. I would direct my students here when it’s time for them to do a research project so that they know how to find and correctly use sources. This site is another good example of NETS-T 1 (b), since it has students working as a real microbiologist would in their career. The guide also does a good job of covering NETS-T 4 (a), by pointing out how to best evaluate the literature, and how to present it in a legal and ethical manner


AMSER – Applied Math and Science Education Repository


This is a repository  that’s extremely relevant to me, since it specifically collects community college-level resources. There is a huge variety of learning activities that could be incorporated to various stages of Biology projects. For example, AMSER linked me to this interactive lesson on aseptic technique, which would be an engaging introduction to lab work. AMSER is a good example of NETS-T 5 (c), because it helps me, the teacher, expand on my knowledge of adequate activities for a community college setting. It is also a good one for NETS-T 2 (a), because they are digital tools – many of them interactive- that can be adapted for my own classes.




Mindmeister is a mindmapping online tool that’s extremely easy to use. It is great for project-based learning because it can help students visualize and structure their ideas creatively, either individually or collaboratively. This tool is a great example of the NETS-T 1 (a) and (c) in action, because this site allows students to model their creativity in a visual way, as well as collaborate with their peers in the process. The tool also represents the NETS-2 (a) since it can be adapted for several learning purposes, while once again promoting self and collaborative creativity.


FreeBIEs – Project Based Learning for the 21st Century


This resource is more geared towards teachers preparing for project-based learning in their classrooms. It includes guides that help us organize the project, plan it on a calendar, prepare a rubric, keep track of project management, etc. FreeBIEs is relevant for NETS-T 3 (a) as it demonstrates a knowledge of technology on the part of the teacher. By using new technology resources, a teacher can act as a leader for students using digital tools in their learning; so these tools are also relevant to NETS-T 5 (b).




I am loving this resource. They include user-uploaded rubrics for all sorts of Biology projects, sorted by grade level. One of the best rubrics I found in iRubric is this Lab Report Assessment which guides students into crafting a well-constructed scientific report. Scientific communication is a huge component of Biology projects. This resource covers all of NETS-T 2. Through this tool you can design your own digital resources for students, and customize them for each group. You can make a more custom and personalized rubric to fit with more student types as it makes it easier to grade and keep track of the students progress. And since the site is great for sharing, collaborating, and pooling data, it can be better used to analyze teaching and learning trends. In addition, as this allows the teacher to contribute their lessons for sharing, it is also a good example of NETS-T 5 (d).


HHMI – Virtual Labs


These virtual labs could become integral to my Biology projects. Some of them are introductions to topics, and in extreme circumstances some could be used as substitutes for wet labs. Although these exercises are meant for individual students, they can be easily adapted for collaborative efforts. This is another good example for NETS-T 1 (b), and (c), as it has exercises that challenge student problem-solving abilities individually or in groups. These virtual labs can be adapted for different classes, and promote creativity through interactive resources, making them a good example of NETS-T 2 (a).


Article 2: Project-based learning for undergraduate students

Title: Increasing awareness about antibiotic use and resistance: a hands-on project for high school students

Author: Maria João Fonseca, Catarina L. Santos, Patrício Costa, Leonor Lencastre, Fernando Tavares

Journal: PLoS One

Publication date: September 12, 2012

Theme for Weeks 4 and 5: Project-based learning for undergraduate students

Antibiotic resistance has become such a hot topic in Biology and Healthcare, that there is an incredible amount of resources available to educate both the general public and specialized students. I chose this project, “Microbiology recipes: antibiotics a la carte”, because it includes a mix of interactive lectures and laboratory activities that covers all the bases in a practical, engaging way.

Let me get this out of the way: the authors intended this project to be carried out by high school students aged 15-17, but I believe that it will have similar benefits in undergraduate students aged 17-20. The main reason they decided to target this to high school students was to help them transition to more sophisticated conceptualizations of bacteria and antibiotics, which might be challenging due to their abstract nature. This level of instruction is ideal for a lower-level undergraduate Biology course.

The project began with an overview of the activities to be performed and basic laboratory safety training. Subsequent lectures provided the background for the wet lab activities, and introduced students to the use of bioinformatics for finding genes that code for antibiotic resistance. Students also analyzed scientific articles to learn about the format for reporting data within the scientific community. The wet labs consisted of acquainting students with basic techniques used for manipulating microorganisms (something I would probably cover at the beginning of my course), and then assaying antibiotic resistance using commercial and natural antibiotics.

The researchers assessed the effectiveness of their project through the use of surveys (pre- and post-project questionnaires), direct observation, and evaluation of artifacts produced by the students. They found that students improved their laboratory skills, refined their knowledge of antibiotic resistance and were eager to share their experience with relatives and friends.

The project facilitated and inspired student learning (NETS-T 1) because students were engaged in a real-world issue, and used digital resources to learn about the science behind antibiotic resistance. Because of the inclusion of bioinformatics tools, I would say it was a digital age learning experience (NETS-T 2). Students developed research and information fluency (NETS-S 3) as they had to evaluate scientific literature to learn about how to use and organize their experimental results .

As an educator, I have covered this topic before, but never in such an encompassing fashion. This article gives me great guidelines to follow when preparing my own antibiotic resistance module.

Fonseca M.J., Santos C.L., Costa P., Lencastre L., Tavares F. (2012). Increasing awareness about antibiotic use and resistance: A hands-on project for high school students. PLoS ONE, 7(9): e44699. doi:10.1371/journal.pone.0044699

Article 1: Project-based learning for undergraduate students

Title: An open-ended, inquiry-based approach to environmental microbiology

Author: Frank Caccavo, Jr.

Journal: The American Biology Teacher

Publication date: November-December 2011

Theme for Weeks 4 and 5: Project-based learning for undergraduate students

As an undergraduate student of Microbiology, most of my classes had a similar format: in addition to lectures, we had laboratories at least once a week where we explored techniques related to the weekly topics. These were self-contained (“cookbook”) lab exercises which were only meant to facilitate skill acquisition and familiarize us with the principles behind the science. This approach shifted when I became a graduate student and we began to tackle collaborative semester-long projects. Caccavo proposes that we follow this model when we teach undergraduate students, and gives a detailed report of his experience implementing this approach.

Student teams were encouraged to pick their own research topics. When they picked wastewater treatment, the instructor covered the content and took the students on a fieldtrip to the local plant: this gave students enough knowledge to be able to narrow down their research topic.

Students were introduced to the scientific method and basic laboratory techniques. Then, they collected literature on the topic so that they could get an idea of what has been done within the field, and think of which angles to pursue experimentally. Their next step was to submit a research proposal in order for them to “organize their thoughts, focus their efforts, and provide a structural framework for the execution of their experiment” (Caccavo, 2011).

At this point, students could finally begin their lab work! This was my favorite part of the learning experience, because undergraduate students often don’t realize that scientific work involves hours of work outside of the laboratory. In the end, as with any research project, they had to present their results to an audience via posters.

Students completing a lab experiment

Image source: University of Pittsburgh at Bradford, from http://commons.wikimedia.org/wiki/File:Science_lab_in_Fisher_Hall.jpg

The project applies many of the NETS standards to the learning experience. Firstly, it facilitated and inspired student learning (NETS-T 1) because the instructor promoted a creative, collaborative environment that had students solving real-world problems. Students demonstrated they could explore a complex issue to produce original research (NETS-S 1, Creativity and Innovation). They developed research and information fluency (NETS-S 3) as they had to gather, evaluate and use scientific literature to plan their project. They improved their critical thinking, problem solving and decision making skills (NETS-S 4) since they were in charge of identifying the problem, developing appropriate questions, and planning and performing all experiments. This is all tied together by communication and collaboration (NETS-S 2).

Two more things make this project stand out for me. The first one is that the instructor is a supporter and not a director- the students are in charge of their own learning.  The second one is that the project helped students decide whether science was something they wanted to pursue as a career or not. As Caccavo puts it, “the best way to learn science is by doing science” (2011), and students should get the chance to experience a real research environment firsthand.



Caccavo, F. (2011). An open-ended, inquiry-based approach to environmental microbiology. The American Biology Teacher73(9), 521-525. doi: 10.1525/abt.2011.73.9.4

Public domain resources

Public domain resources are hard to find and use in Biology because once we cover the basics, we move on to current research- most of which is copyrighted or shared under Creative Commons. Nevertheless, I managed to find some resources that I could use in my classroom.

The Biodiversity Heritage Library
This e-library contains over 50,000 natural history works (such as Charles Darwin’s famous “On the origin of species by means of natural selection”) both in the public domain and under CC.

Smithsonian Institution’s Flickr
The Smithsonian provides images both in the public domain and under CC. Many of these would be an excellent addition to any science lecture- for example, images from the Portraits of Scientists and Inventors.

US Food and Drug Administration
Since it is published by the government, text and graphics in this website are public domain. This is a great place to find booklets that can aid instruction of introductory and advanced Microbiology, such as the Bad Bug Book.

US Fish and Wildlife Service National Digital Library
A government-published collection of wildlife materials. The videos and documents are a source of information on various animals, diseases connected to them, and their interaction with the changing environments. There are several excellent resources that link this education to real world use.

National Center for Biotechnology Information – Bookshelf
Provides access to Biology and Health Care books; much of the content is authored and published by the the US government, and occassional copyrighted material is especially marked. Great resource for students of Medicine or General Biology.

Medline Plus – A service of the US National Library of Medicine
A good source of medical pictures, diagrams, videos and descriptions. The topics range from general anatomy to various diseases.

The CDC Image Gallery
A very wide range of images and articles mostly centered around health, but going in depth about the particular maladies and risks. The health risks can also be sorted by age and lifestyle to narrow down a topic. These can be linked to assist in class presentations.

U.S. Geological Survey
A mostly public domain site with excellent Biology and Microbiology photos, as well as teaching resources (videos, lectures) for different student groups.

National Cancer Institute
A good collection of various anatomy and cellular pictures. There are also some nice stock photos covering general science and technology.

Public Domain Images
A collection of public domain photos of very high quality. The Biology and Medical Science photos can be of use in lectures and digital presentations.

Creative Commons resources

A primary source is a document or physical object written or created during the time under study. Some examples of primary sources are interviews, speeches, manuscripts, news film footage, original creative works, and relics or artifacts. A secondary source, on the other hand, is one that interprets a primary source, such as textbooks and magazine articles.

In my discipline, Biology, our primary source is original research in the form of conference papers, lab notebooks, patents, studies, surveys, proceedings, theses and dissertations. My experience in teaching and learning Biology has involved both primary and secondary sources: we follow a textbook but supplement instruction with original texts, images and video, and learn about innovative research via journal articles.

The internet has made primary and secondary sources universally available; these are some of the materials and tools I’ve found under the Creative Commons (CC) license.

All of these resources are related to the NETS-T 2: Design and Develop Digital Age Learning Experiences and Assessments, which asks teachers to incorporate digital resources into the learning experience. Also, because they are under Creative Commons licenses, they Promote and Model Digital Citizenship (NETS-T 4) as the use of these materials exhibits respect towards intellectual property.


Public Library of Science (PLoS)
PLoS provides a huge variety of scientific journals online. One neat feature is the PLoS blogs, which features scientist sharing their research a little more informally.

BioMed Central
Self-styled “the open access publisher”, another provider of scientific journals which are available online immediately upon publication.

Nature Publishing Group (NPG)
Only certain journals under the NPG are published under CC:  Molecular Systems BiologyClinical and Translational Gastroenterology, and Cell Death and Disease. Plus, any article that publishes the genome sequence of an organism for the first time falls under CC as well.

Open educational resources

Many higher education institutions provide course materials (lecture notes, exams, videos) for free under CC. The OpenCourseWare Consortion attempts to list all of these courses in their website. Some major contributors of course materials for Biology are:

MIT OpenCourseWare

Tufts University OpenCourseWare

Utah State OpenCourseWare

Open Learning Initiative at Carnegie Mellon

Johns Hopkins school of Public Health OpenCourseWare

Webcasts by the University of California, Berkeley

Open Yale courses

Khan Academy

The Open University


 Tools & Media

The MicrobiologyBytes Video Library
This gallery hosts hundreds of Microbiology videos which would help students visualize the microbial world.

Wolfram Demonstrations Project
This website hosts interactive illustrations that can be used to visualize complex concepts. (While you’re here, stop by WolframAlpha to calculate nearly anything! )

The MicrobeLibrary from the American Society for Microbiology
This website hosts a variety of resources that could be used to enhance lecture or lab presentations (images, videos and animations), plus a useful Critical Thinking Question Bank is in the making!

Open Wetware wiki
This wiki is maintained by many research groups around the world and hosts mainly biological protocols for laboratory research.

OER Commons
This website is a repository for user-uploaded resources such as lectures, games, assignments, lesson plans, syllabi, training materials, etc.

MERLOT (Multimedia Educational Resource for Learning and Online Teaching)
Similar to OER Commons, MERLOT houses a variety of learning materials for tens of disciplines. All the content is licensed under CC.


Copyright, Fair Use, and Creative Commons

In order to appropriately use internet resources in accordance with the NETS standards, students and educators must have a good understanding of copyright law and “fair use”. I will summarize my understanding of these topics here for future reference.

Hall Davidson explains that fair use is using a resource for the greater good of society, superceding the ownership rights of the copyright holder. All of these scenarios constitute fair use: commenting, news reporting, teaching, scholarship and research. There are also guidelines in place for multimedia use, which in general ask that the public use 10% or less of the entirety of the work. It goes without saying that any and all materials must be legitimately acquired and the user must give proper citation.

Image source: Thomas Scovell, retrieved from http://commons.wikimedia.org/

The new Creative Commons license allow people easier access to research, education, and culture. They are less restrictive (“all rights reserved” vs “some rights reserved”), and eliminate the need to ask the creator permission to use their work. Creative Commons explicitly give people the right to share, use and build upon a work, on the conditions of the creator. As an artist, I use Creative Commons when I upload my art to the internet.

Image source: Screenshot from http://www.deviantart.com/submit/deviation

I agree with Larry Lessig’s stance. Nowadays, as he says, ordinary people break the law as a result of actions as simple as sharing a picture on their facebook page. We need to switch to a different, more open model that allows us to share freely.

I personally wouldn’t show the “YouTube Copyright School” video in a classroom; it’s a little too cutesy, and focuses mostly on Youtube’s policy rather than the big picture. I’d prefer to show Hall Davidson’s videos on copyright. Here is a video on Creative Commons that I found enjoyable and relevant enough to use in a classroom:


Creative Commons – About. Retrieved from http://creativecommons.org/about

Digital citizenship

Who will you be online? This video offers a cute introduction to digital citizenship. Bully or protect? Safe or sorry? Credit or steal? The choices are clear, and it is what responsible citizens do in their everyday lives. Cyber bullying, in particular, has been a hot topic in the last decade. According to the Pew Internet report on “Teens, kindness and cruelty in social network sites”, certain groups have experienced more unkindness than others (teenage girls aged 12-13 and black teenagers), and even when they don’t encounter hostility, most teens know that the online world can be “crude”, “mean” and “fake” (Lenhart et al., 2011). Online harassment has been blamed for the suicide of many teens.

Schools are already teaching ethics and citizenship so that students can navigate the real world. It is time we start teaching digital citizenship, ideally from a young age, in order to guide students into reaching the NETS-S standards. I envision this happening first in higher education rather than in K-12 classrooms. A quick browse of Coursera’s online classes show some relevant courses: “E-learning and Digital Cultures“, “Securing Digital Democracy“, and “Networks: Friends, Money, and Bytes“.

(As a side note for those who don’t know, Coursera offers online higher education from world-wide recognized universities for free, in what is called “massive open online courses” or MOOCs. You can read more about it here!)

The elements of digital citizenship as described by this video (and their website) are:

  • Participation in online society, including use of digital commerce and exchange of information.
  • Digital literacy, knowing when and how to use technology.
  • Digital etiquette.
  • Knowing technology law, rights and responsibilities.
  • Monitoring your health and wellness as related to the mental and physical effects of technology use.
  • Taking electronic precautions to guarantee safety.

These correlate nicely with the items that the fourth NETS-T standard advises educators to teach in order to promote digital citizenship.

Wagner’s inventory of skills that students need for the future is exactly the same as the list of NETS-S standards, except that the latter clearly spell out “digital citizenship” as a required proficiency while Wagner seems to gloss over it. His list includes problem-solving skills, collaboration, adaptability, initiative, effective communication, imagination, and accessing and analyzing information. Wagner stresses that learning should not only be based on content; teaching these skills is important too. When we think of digital citizenship, it is the same case: it’s not about the information, but about how we access it, how we use it, how we communicate it, and how we conduct ourselves online.


Lenhart, A., Madden, M., Smith, A., Purcell, K., Zickuhr, K., & Rainie, L. (2011). Teens, kindness and cruelty on social network sites. Pew Internet & American Life Project. Retrieved from http://www.pewinternet.org/Reports/2011/Teens-and-social-media.aspx

Privacy and security in the technological world

Google, Yahoo! and other search engines collect and store consumer information to personalize our online experience —this is what Eli Pariser calls a “filter bubble” that restricts the information shown to us—. Colleges and employers may accept or reject applicants based on their facebook profile –some employers are even demanding passwords from job applicants. Online street maps and simple facebook updates become a tool of surveillance and can even help solve crimes. These digital tools are both providing a service and invading our privacy. It is a world of trade-offs, like Bruce Schneier explains in his talk.

Hasan Elahi speaks of the trouble he went through when authorities believed him a terrorist. He began to compile data of everything about his life to supply to the FBI: transportation logs, communication records and financial data. “By putting everything about me out there, I am simultaneously telling everything and nothing about my life”, he tells The New York Times. “Despite the barrage of information about me that is publicly available, I live a surprisingly private and anonymous life”. This happened in 2003, and people wondered why anyone would share so much of their personal information. Nowadays, few of us think twice about sharing what we are doing at all times.

What does this all have to do with education? Privacy and security concerns are related to the fourth NETS-T standard, “promote and model digital citizenship and responsibility”, which recommends teaching the safe use of digital information. It is especially important to teach this to the younger generation, who has grown up accustomed to broadcasting their lives to the world. Additionally, the third NETS-T standard, “model digital age work and learning”, advises teachers to effectively use tools to locate and evaluate information resources to support learning. These information resources can sometimes come from a simple tweet, facebook post, or reddit thread. I will address the concept of digital citizenship more fully in the next post.


Associated Press. (2012, August 1). Illinois facebook law makes it illegal for employers to ask for logins. Huffington Post. Retrieved from http://www.huffingtonpost.com/2012/08/01/illinois-facebook-law_n_1730077.html

Elahi, H.M. (2011, October 29). You Want to Track Me? Here You Go, F.B.I. The New York Times. Retrieved from

Hill, K. (2012, July 20). Those at ‘Dark Knight Rises’ shooting turn to reddit for support. Forbes. Retrieved from http://www.forbes.com/sites/kashmirhill/2012/07/20/batman-shooting-reddit/

The NETS standards, collaboration and communication

I have had the chance to teach lower-level Biology courses to traditional college students aged 17-21 ; all of these young people (and myself) belong to the generation known as “Millennial”. We have grown with the increased presence of technology, information and media from a very young age, and require a certain level of connectedness with our family and friends via digital devices and services. We are used to getting information from a simple Google search and switching from activity to activity quickly (McMahon & Pospisil, 2005).

The 2011 Horizon Report acknowledges the role of the internet in teaching and learning. People expect to switch from work, to study, to leisure with minimal readjusting time. As educators, we need to find ways to keep the students engaged and keep pace with the proliferation of information, tools and devices. Many teacher preparation programs already require a level of literacy in digital media, and the Report suggests more universities should follow suit. The main problem would be that digital technologies change too rapidly, making curriculum development difficult. Some technologies that the Report mentions will become mainstream in education are e-books, mobile-devices, game-based learning, movement-based computing (such as the Kinect), augmented-reality learning (such as Second Life), and the use of learning analytics (Johnson, Smith, Willis, Levine & Haywood, 2011).

The NETS standards were developed by the International Society for Technology in Education (ISTE), constituting a set of skills and knowledge necessary to teach and learn effectively in the digital era.

The NETS-T are:

  1. Facilitate and inspire student learning and creativity.
  2. Design and develop digital age learning experiences and assessments
  3. Model digital age work and learning
  4. Promote and model digital citizenship and responsibility
  5. Engage in professional leadership

The NETS-S are:

  1. Creativity and innovation
  2. Communication and collaboration
  3. Research and information fluency
  4. Critical thinking, problem solving and decision making
  5. Digital citizenship
  6. Technology operations and concepts

This week we are focusing on communication and collaboration. Howard Rheingold and Stefana Broadbent have talked about our ability to broadcast our thoughts to a huge number of people at the click of a button- just like I am doing right now. We use email, instant messages, mobile phone calls and video conferences to communicate with friends, family and peers. This trend in communication was only more obvious to me when I read about researchers analyzing billions of phone calls and texts from mobile devices to find that mothers favor a relationship with their adult daughters rather than with their husbands (Palchykov, Kaski, Kertesz, Barabasi & Dunbar, 2012).

Rheingold further talks about collaborative technologies that could possibly be used in a classroom such as forums, wikis, blogs and usenet groups, that allow people to interact with many of their peers at once rather than one-on-one.

The suggestion to substitute “customer” for “student” in the “Effects of Social Media in Communication” video tickled my funny bone.

Nowadays, students demand to be engaged by their instructor and require instant feedback. They have short attention spans and the responsibility falls on the instructor to keep them stimulated. I have seen these characteristics reflected in some of my teaching evaluations:

“Always to the point and a fair grader. Returns graded work to students quickly. Doesn’t waste our time.”

“The learning environment is very involved”

“Gets us in and out efficiently”

As a teacher I believe that the NETS standards are a great foundation for building an engaging classroom for the Millennial student.


Johnson, L., Smith, R., Willis, H., Levine, A., and Haywood, K., (2011). The 2011 Horizon Report. Austin, Texas: The New Media Consortium.

McMahon, M., & Pospisil, R. (2005). Laptops for a digital lifestyle: Millennial students and wireless mobile technologies. ASCLITE 2005

Palchykov, V., Kaski, K., Kertesz, J., Barabasi, A.-L., & Dunbar, R.I.M. (2012). Sex di fferences in intimate relationships. Sci. Rep. 2, 370.

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