proposal

=CI Team: Using Cyberinfrastructure in Blogs, Wikis, and other RSS Technology to Promote Open Source Science in Higher Education and Workforce Development= =(draft in progress)=

[|Jean-Claude Bradley], Principal Investigator

[|Beth Lynne Ritter-Guth], Co-Investigator

Abstract
The objective of the CI Team is to develop an enhanced cyberinfrastructure for the promotion of open source science in higher education and for workforce development. Through the development of innovative methodologies utilizing Blogs, Wikis, and other RSS Technology, the CI-Team will facilitate open source science initiatives to communicate with other scientists and the general public. As a response to the National Science Foundation's call "to create, deploy, and apply cyberinfrastructure in ways that radically empower all scientific and engineering research and allied education," this proposal attempts to connect two diverse populations in open source science research and dissemination (1). The first goal is to execute and communicate scientific research effectively by minimizing the publishing time of routine experiment findings through the use of cyberinfrastructure. By relying exclusively on popular social software like blogs and wikis, scientists can utilize open source cyberinfrastructure to publish experiments in real time while generating solutions quickly, efficiently, and for little cost. The second goal of the CI Team is to partner and educate undergraduate and graduate students from two vastly different schools on the uses of cyberinfrastructure in open source science in an effort to prepare them for the workforce. Students from Drexel University's selective chemistry program will be partnered with students in open enrollment Applied Science degree programs at Lehigh Carbon Community College. These students, at various stages of their academic experience, will operate as a learning community by identifying, understanding, and addressing the needs of global scientists. Further, they will learn to communicate complicated scientific terms to the general population by using podcasting, vodcasting, screencasting, blogs, and wikis to share information. The final goal of the CI Team is to educate faculty in higher education on the uses of cyberinfrastructure, specifically the uses of blogs, wikis, and RSS technologies, in the disciplines of science. By presenting open source talks and workshops, faculty members will understand the importance and uses of open source science initiatives. Further, they will be provided immediate access, through open source cyberinfrastructure, to teaching and learning materials. Funding by the National Science Foundation is needed for the acquisition of robust laptop computers required to run social software and programs designed to provide podcasting, vodcasting, and screencastig formats. Further, funding is needed to support student scholarships at the undergraduate and graduate levels. Funds to support automation and lab supplies are necessary to conduct comprehensive research. Finally, money to support travel for students and Investigators is needed.

Introduction
Historically, chemical research has been communicated ineffectively. Most experiments remain unpublished because current publishing trends require that only the most polished experiments be presented. Cyberinfrastructure, in the form of open source chemistry, provides real time publishing and allows chemists to quickly build upon the research of others. In addition to efficiency, this research can be published for little or no cost by using wikis, blogs, and other RSS technologies. Open source science initiatives allow for students and professionals to collaborate and disseminate information openly. In collaborating with others within the chemistry community, it may be possible to produce new drugs or other chemical solutions quickly and efficiently.

Open source scientific research is a new approach and is "a way of fixing the patent problem" (2). The patent procedures require withholding pertinent information from the public as a means to secure patenting and commercial funding. As a result, crucial information is lost in the process, and neglected diseases continue to spread and worsen. Open source projects like the [|Institute for One World Health] (3) (a non profit pharmaceutical company) and [|Find-A-Drug] (4) attempt to provide quality solutions to the neediest of problems. Additionally, the following collaboration initiatives are attempting to contribute to humanitarian science solutions:

1. [|The Synaptic Leap] 2. [|Chemists Without Borders] 3. [|World Community Grid] 4. [|BioForge] 5. [|CODATA] 6. [|ACS Chemical Biology Wiki] 7. [|The OpenScience Project] (software)

The UsefulChem initiative is unique in that it is completely open sourced. Students will publish all of their work in real time, including successes and failures, to demonstrate the power of open source collaboration. The sharing of this information, through cyberinfrastructure, promotes the idea that open collaboration fosters intelligent revision and purposeful solutions. Professional (workforce) initiatives, combined with the UsefulChem Project, provide various perspectives for examining the world's greatest problems. As a collaborative community, we can disseminate information quickly to our colleagues within the chemistry community and beyond. Since the communication platforms are free through the use of wikis and blogs, these measures for sharing information are entirely cost effective, as well.

As students post work in a collaborative and open format, they will need to establish strong written communication skills. As the National Science Foundation indicates, "collaboratory environments built on cyberinfrastructure can enable people to work routinely with colleagues at distant institutions, even ones that are not traditionally considered research universities, and with junior scientists and students as genuine peers, despite differences in age, experience, race, or physical ability. These new environments can contribute to science and engineering education by providing interesting resources, exciting experiences, and expert mentoring to students, faculty, and teachers anywhere there is access to the Web" (1). By partnering science majors enrolled in writing courses at the community college level with junior and senior chemists at a four-year research institution, this project meets the basic goals of the Cyberinfranstructure grant.

Objectives of Project
The objectives of the project are to utilize cyberinfrastructure to:


 * 1) Design, implement, sustain, and assess an open source science project using blogs, wikis, and other RSS technologies;
 * 2) Execute the chemical synthesis component in the Drexel lab;
 * 3) Facilitate efficient communication of the scientific results and discussions to the wider community rapidly and effectively using podcasting, vodcasting, screencasting, blogs and wikis;
 * 4) Communicate all steps of experimentation, even those not published in traditional scientific literature, such as failed experiments, so that scientists and students can learn from the mistakes of others;
 * 5) Communicate all levels of scientific discourse, even if that knowledge is incomplete or speculative;
 * 6) Communicate the thinking behind the chemistry by publishing the brainstorming efforts that take place in generating ideas (e.g. synthetic design);
 * 7) Extend automated processing of molecular properties to other open standards being promoted by the cheminformatics community, notably Chemical Markup Language (CML);
 * 8) Educate undergraduate (LCCC, Drexel) and graduate level chemistry students (Drexel) on the uses of cyberinfrastructure in academic and workplace environments;
 * 9) Educate undergraduate (LCCC, Drexel) and graduate level chemistry students (Drexel) on the benefits of open source science initiatives;
 * 10) Educate undergraduate (LCCC, Drexel) and graduate chemistry students (Drexel) on the technology tools of the 21st century workforce by teaching them to use podcasting, vodcasting, screencasting, blogs, and wikis to communicate complicated material in plain language;
 * 11) Educate faculty in higher education on the uses of cyberinfrastructure as a teaching tool in science and technology;
 * 12) Network with other non-profit and humanitarian initiatives working toward open source science;
 * 13) Create open source partnerships with colleagues at Drexel, LCCC, and other institutions of higher education;
 * 14) Identify areas for further scientific study; and
 * 15) Create a system that can be replicated by anyone at little or no cost.

Problem:
In April 2006, [|Biopeer], a life science community blog, reported that "malaria kills one million people globally every year and is especially prevalent in developing countries (5). The World Health Organization (WHO) "has declared a state of emergency against malaria, TB and HIV/AIDS in the world and has asked its member countries to try and control these deadly diseases by 2015. If the recent researches successfully lead to production of low-cost anti-malaria drugs, a vast population from the developing countries would stand to benefit" (3B). They also report that "although Africa is most affected by malaria, Northeast India is also a known malaria zone, with the disease claiming an estimated 500 lives annually. At least 50 people have died since the beginning of April [2006] and up to 25,000 affected in a malaria epidemic in northeast India's Assam" (3). Clearly, new solutions to the malaria problem are needed to support these existing science initiatives. The UsefulChem Project can aid this scientific community, for example, because results will be published in real time, and other scientists, from a variety of disciplines, can access the information (6). As a collaborative community, all open source scientists will be able to work together to solve the world's neediest problems.

Another important example for the need for open source science initiatives is extracted by the US government's call for action regarding issues like malaria. In June 2005, President Bush released the [|President's Malaria Initiative] (PMI). This initiative is "a U.S. government program designed to cut malaria deaths in half in target countries in sub-Saharan Africa" (7). In support of his initiative, he "pledged to increase U.S. funding of malaria prevention and treatment in sub-Saharan Africa by more than $1.2 billion over 5 years. He also called on other donors; foundations; and private, public, and voluntary organizations to complement the U.S. commitment by providing additional funding" (7). The information provided by the UsefulChem Project will be available in "real time" to those working most closely with the affected populations identified in this plan. This response time meets the needs of the global community, and, as such, satisfies, in part, important existing initiatives like [|President Bush's Malaria Initiative] program and will, as a result, create and support the NSF's desire to provide "tools and services...enabling individuals, groups and organizations to advance science and engineering in ways that revolutionize //who can participate, what they can do//, and //how they do it//" (8).

Research/Pedagogy:
The Blue Ribbon Advisory Panel on Cyberinfrastructure indicates that a "central goal of ACP is to define and build cyberinfrastructure that facilitates the development of new applications, allows applications to interoperate across institutions and disciplines, insures that data and software acquired at great expense are preserved and easily available, and empowers enhanced collaboration over distance, time and disciplines" (1). Open Source Science (also called Open Access Science) meets these demands. The groundbreakers in this field, Henry Rzepa, Peter Murray-Rust, John Mitchell, and Marion Cass, have championed the concepts of opening the science field for the betterment of all. The problem has been that "most chemical information is closed and cannot be re-distributed without permission. This has led to a failure to adopt modern informatics and software techniques and therefore paucity of chemistry in bioinformatics" (9). Technology, especially those used to open source science, "offers the hope of making chemical data (compounds and properties) free during the authoring process" (10). They "argue that the technology is already available" and that, by utilizing this technology, greater advances can be made in chemistry (and, assumedly in all science).

Rzepa and Cass assert that "a greater emphasis on data capture and its re-usability, together with the use of opensource software...can result in a much more meaningful and future-proofed way of presenting chemical knowledge to students" (9). Further, they indicate that the use of wikis and podcasts (distributed through blogs) are an efficient and cost effective mode of knowledge transportation (9). The main thrust of their movement toward open source science is that "the benefits of open access include higher quality, greater availability, and development of the Biochemical Semantic Web where robots mine text and data as a basis for knowledge-driven science" (10). They "argue that funders, institutions, authors, editors, publishers and readers will all benefit" (10).

In conjunction with the ability to share pure science through open source initiatives, it will become increasingly important for scientists to communicate effectively in writing to an expanded and diverse population. However, the writing skills are sometimes lacking; "according to the report of the National Commission on Writing in America's Schools and Colleges (2003), there is a specific deficiency in the writing skills of high school and college graduates, especially among engineering and science students" (11). Frederick Dormshak, a specialist in Animal Sciences at Oregon State University, recently told graduates that "scientists...are asked more and more frequently to describe the results of [their] technical research in written form understandable to the lay public—the same lay public that includes representatives of state and federal legislatures responsible for allocating money for agricultural research. It is obvious that good writing skills are a requisite for success in science" (11). The need for strong writers is true in all disciplines, but, certainly, emerging scientists need the opportunity to partner real science with comprehensive writing tasks. Dr. Dormshak rightly believes that "as educators...we need to be cognizant of the importance of writing skills and pay extra attention to ensuring that our graduates are able to effectively communicate via the written word. Their survival in the professional world will certainly depend on this skill" (11).

Current Implementation:
The UsefulChem Project was initiated at Drexel University in July 2005 by searching to identify current important problems with chemical solutions. The synthesis of novel anti-malarial compounds was quickly identified as a pressing need. Due to the high prevalence of the disease, other initiatives aiming to coordinate open source science have found (independently) that malaria is a high priority target. Find-A-Drug provided a library of 220 predicted inhibitors of enoyl reductase, an enzyme used by the malaria parasite to build its cell wall. The synthesis was researched and debated online in a Drexel-based blog before synthesis began in the lab. Three Drexel graduate students and four undergraduate students joined the project, began experiments, and their work is recorded in a blog format. To date, ten experiments have been conducted on [|enoyl reductase]. Each experiment is detailed on the UsefulChem Experiments blog. Once the inhibitors are made, they will be tested in vitro in the Drexel Medical School.

In May 2006, the first section of Technical Writing (LCCC) was joined with Drexel Chemistry students. These students, as a test group, were not identified as specifically science majors. The UsefulChem project was offered as an alternate project to the standard service project for the course. In preparing materials for the course, several employers, including profits and non-profits, were contacted to determine the writing needs of science majors. All of the companies indicated the desperate need for strong science writers that could convey technical material to both technical and non-technical audiences. Students at LCCC and Drexel were partnered, via a blog and wiki, and worked together to prepare a foundation for the project.

In August 2006, a new group of writing students will be partnered with Drexel chemistry students. They will continue to provide scaffolding for the project. In January 2007, the first group of AAS students will be partnered with Drexel chemistry students.

Current Impact
The science community has provided positive feedback to our current initiatives. For example, a chemist from the University of Sydney commented on one or our experiments while it was still in progress. The speed of this type of feedback is usually only possible for groups of scientists already in close collaboration. Chemrefer contributed by finding articles about the compatibility of some chemical groups, guiding our synthetic strategy as we are still planning it. Referring URLs on [|www.sitemeter.com] demonstrates how many people are finding the UsefulChem blogs. Further, they illustrate location of searchers (12). As of May 19, 2006, there were 6,616 page visits in the UsefulChem site since its inception, By month, the following usage has been tracked through [|www.sitemeter.com]:



Generally speaking, any number of people can access this information for a variety of reasons, The more telling data is extracted by examining the usage numbers of the experiments blog. Since its inception in January 2006, 2,242 page views were noted. As of May 19, 2006, the following monthly usage was reported:

Presently, most people access the information through Google searches for chemicals or reactions. This data is also tracked through [|www.sitemeter.com] ; as the following chart suggests, only a small portion of the visits come exclusively from Drexel (25%) and LCCC (2%):



The UsefulChem Wiki has also experienced high traffic since its inception in Decemb 2005. As of May 19, 2006, over 27,500 page views were tracked by wikispaces.com. Clearly, the current impact is reaching an international audience.

If the trend continues, more students and professional scientists will access the open source information presented on the blogs. As such, the information presented in these formats should have the strongest foundation, the best RSS technologies, and the most comprehensive and usable language.

The workforce community has responded well to the idea of training scientists to be strong writers. In informal interviews, several participants indicated that the strongest need in the industry is scientists that communicate to both technical and non-technical audiences. Since many of the AAS students will gain entry into the job market after two years of study at LCCC, the idea of English courses designed specifically with their career goals in mind was appealing. For example, an emphasis on CSE and not MLA formatting was indicated as an essential workplace skill.

The pilot writing project began on May 15, 2006. In the short time between the inception of the UsefulChem Writing Partners Blog and May 19, 2006, there were a total of 163 page views. While it is certainly too early to determine the usefulness of the UsefulChem Writing Partners Blog, it is certain that expanded exposure will be an effective community tool.

Description of Partnering Institutions
Drexel University is Philadelphia's technological university and is among the top 50 private, non-profit, national doctoral/research universities in the US, and is ranked by US News & World Report as one of //America////'s Best Colleges for 2006//. Drexel consists of 11 colleges and schools offering 161 degree programs to approximately 16,000 students. It has over 90,000 alumni and 1,000 full-time faculty members. Founded by financier and philanthropist Anthony J. Drexel in 1891, Drexel has been a leader in the integration of technology into academics. Drexel University's academic distinctions include several top rankings in Engineering and a top 10 ranking in Library and Information Science (No. 1 for specialized programs in information systems).

At Drexel University, students enrolled in organic chemistry will participate in this project. They will have access to instruments, supplies, and other equipment needed to conduct experiments. They will have access to loaner tablet PCs to communicate with students at LCCC and to publish their experiments on the class blog. They will learn to utilize the free social software to communicate with students at LCCC. They will learn to utilize the tools of podcasting, vodcasting, and screencasting to fully understand the tools used to open source science. They will learn to translate materials into various formats including iPod technologies. Most importantly, these students will learn to effectively communicate with people at various levels of scientific experience by collaborating daily, weekly, and monthly with LCCC students.


 * In order for quality scientific studies to be performed, the PI will work closely with the graduate and undergraduate students participating in the project. Their collective research will be posted daily via of blogs and wikis.** Interaction with other chemists via all of the cyberinfrastructure tools described in this proposal will be encouraged and monitored.

Lehigh Carbon Community College (LCCC) is a comprehensive, two-year, publicly supported community college whose mission is “responding to the community with high quality education through open access and affordability.” Accredited by the Middle States Association of Colleges and Secondary Schools, the college offers 18 transfer associate degree programs (A.A. and A.S.), 58 career associate degree programs (A.A.S.), 34 certificate programs, and 16 specialized credit diploma programs. The college enrolls over 9,000 credit students annually, and these students represent a diversity of academic abilities, economic levels, and backgrounds. Within the science community, open source research makes sense; it is practical, efficient, and cost effective. However, another layer of understanding is necessary for the research to make sense to the larger community. By partnering graduate and undergraduate chemistry students at a selective four-year research institution with first year rhetoric and composition students majoring in chemistry or chem-tech at an open enrollment community college, the UsefulChem Project will be understood by students at all levels of the academic process. Their experience in sharing information will foster a fundamental desire to open source scientific knowledge. In meeting their course objectives, these students will have the opportunity to collaborate with real scientists and emerging writers, explore important issues from different perspectives, and, together, disseminate information to the global community. Students will discuss and address the concepts and ethics of intellectual property. Foundationally, they will root their academic careers in a shared professionalism and commitment to the needs to the community.

At Lehigh Carbon Community College, students will be selected for this project based on academic major and performance indicators. Students in science majors, specifically students enrolled in the Applied Science Chem Tech Program, will be identified to take the target courses (Composition and Technical Writing). These courses will be identified by an "S" indicating closed enrollment to science majors. Compass placement scores, high school rank, PSSA scores, and (when possible) SAT/ACT scores will be used to establish placement. Preference will be given to students from impoverished school districts, and students with identified disabilities, minority, and female students will be encouraged to apply.

All students registered in these fundamental English classes will receive a loaner tablet PC for the duration of their studies in English and Science. They are expected to use these laptops for writing demands associated with the project and will utilize the free social software to communicate with students at Drexel. Further, they will learn to use the tools of podcasting, vodcasting, and screencasting to disseminate information about the project. They will detail their research, questions, and materials on the class blog (http://www.usefulchemwritingpartners.blogspot.com) and wiki (http://usefulchem.wikispaces.com/wp). Students will learn to translate all materials into various formatting styles including emerging iPod technologies. Most importantly, students will learn to collaborate, daily, with students at Drexel. Daily and weekly meetings will be held through blog and wiki technology. Monthly meetings will be held using video-conferencing technology.

The Investigators will work collaboratively to design, maintain, and assess student work at both institutions. Further, they will each identify more collaborative partners within their own institutions. The investigators will also work together to publish open source teaching materials in Chemistry and English using wikis and blogs. The investigators will present at nationally recognized conferences on the open sourcing of science and bridging the gap between science and workplace writing through the use of blogs, wikis, podcasts, vodcasts, and screencasts. Finally, they will encourage faculty from other colleges and universities to embrace dual-collegiate learning communities, open sourced education initiatives, and the use of cyberinfrastructure in the college classroom.

The modularization of the reporting of science information makes it much easier to disseminate it to machines in addition to humans. For example, by using a separate blog listing each molecule of interest to the project as a separate post, the processing of much of the related chemical information can be done in batch mode. One graduate student's project in the Drexel team is to develop software to process such information to be useful to other members of the cheminformatics community. Currently, using Visual Basic for Applications code, the entire molecules blog can be imported into an Excel spreadsheet, and web services or local programs are queried to populate the sheet with molecular properties such as molecular weight, commercial availability, SMILES codes, InChI codes and 2D images. One of the objectives of the UsefulChem project is to extend this automated processing of molecular properties to other open standards being promoted by the cheminformatics community, notably Chemical Markup Language (CML).
 * Cheminformatics and Automation**

Grant Methodology, Section C: Proposed Assessment
Successful completion of this grant will be the global use of information presented on the UsefulChem wiki and blogs. Further, the use of cyberinfrastructure tools as they apply to higher education and industry will determine the effectiveness of the open source science materials. By tracking the number of visits, discussions, presentations, talks, and partnerships, the NSF will clearly appreciate the impact of a project of this nature. Since this initiative is a relatively new platform, it is difficult to establish benchmark indicators. However, success will be measured by the ongoing collaborative efforts established within the grant period and extending beyond the grant period. In addition to these overall indicators, the following institutional benchmarks have been placed:
 * 1) Tracking of student materials created and maintained (podcasts, vodcasts, screencasts) will be publicly accessible on the following open source formats:
 * 2) Project Wiki: [|http://www.usefulchem.wikispaces.com]
 * 3) Project Blog: [|http://www.usefulchem.blogspot.com]
 * 4) Experiments Blog: [|http://usefulchem-experiments1.blogspot.com]
 * 5) Writing Partners Wiki: http://usefulchem.wikispaces.com/writingpartners
 * 6) Writing Partners Blog: [|http://usefulchemwritingpartners.blogspot.com]
 * 7) Tracking of the discussion relating to chemical synthetic strategy will be documented on the Main UsefulChem Blog: [|http://usefulchem.blogspot.com]
 * 8) Tracking of experimental results will be documented on the Experiments blog: http://usefulchem-experiments1.blogspot.com/
 * 9) Podcasts, vodcasts, and screencasts will be available for the public on
 * 10) iTunes
 * 11) Project Wiki: http://usefulchem.wikispaces.com
 * 12) Project Blog: [|http://usefulchem.blogspot.com]
 * 13) Writing Partners Blog: [|http://usefulchemwritingpartners.blogspot.com]
 * 14) Tracking discussions about the philosophy and legal ramifications of open source science initiatives will be available for the public on the UsefulChem Writing Partners Blog: [|http://usefulchemwritingpartners.blogspot.com]
 * 15) Tracking the number of presentations, talks, papers, and professional development initiatives will indicate effectiveness of outreach efforts (Goal: 3 presentations per academic year, 3 articles over grant period);
 * 16) Tracking the number of contacts and discussions with other non-profit and humanitarian initiatives working toward open source science will indicate effectiveness of outreach efforts (Goal: 3 partnerships per academic year); and
 * 17) Tracking faculty partnerships at host schools and in the larger academic community will demonstrate effective outreach techniques (Goal: 3 partnerships per academic year in host institutions, 3 partnerships per academic year at other colleges and universities.

Grant Methodology, Section D: Funding Needs
In an effort to prepare and present responsible collaborative research to the Cyberinfrastructure community, consistent funding is necessary. Lab equipment, chemicals, and supplies are essential to the work of the chemistry students learning and sharing information at Drexel University.

The challenges faced by students at Drexel are tied directly to the lack of funds. No graduate assistantships are set aside for work on this project, and the department is not able to sustain the costs of instruments, equiptment, and supplies. In order to provide comprehensive research experiments to the public, it is essential to have graduate level research students working in the lab. Both graduate and undergraduates will also need access to tablet PCs. microphones, PC Cameras, laser printers, and software programs like Camtasia (TechSmith) and Adobe. Finally, in an effort to make sure all materials are available in the most current formats, students will need to produce documents in iPod formats; therefore, students should have access to iPod technology.

The challenges faced at LCCC are the limited tools for technology. Podcasting, vodcasting, and screencasting require tablet PCs, microphones, PC cameras, laser printers, and software programs like Camtasia (TechSmith) and Adobe Writer. Finally, in an effort to make sure all materials are available in the most current formats, students will need to produce documents in iPod formats; therefore, students should have access to iPod technology. Funding for travel will allow students at LCCC to travel to Drexel's lab to meet scientists and learn more about the experiments. Finally, student scholarships will make it possible for needy students, especially minorty students, students with disabilities, and women, to gain entry into an AAS program.

Funding for the PI and Co-PI is necessary to support outreach initiatives. Their efforts to educate others on the uses of cyberinfrastructure in higher education and workforce development will require travel and participation in nationally recognized conferences.

Conclusion
The UsefulChem Project meets all of the tenets of the National Science Foundation's Cyberinfrastructure grant. By teaching students the necessary technologocial tools of the 21st century workforce,