So Many Research Scientists Doing Well

 

2016StudentOutcomes

The New York Times added (yet again) to the many articles about the oversupply of biomedical PhDs looking for jobs as professors.  This new article is titled, “So Many Research Scientists, So Few Openings as Professors.”

The article concludes with this advice, “For those thinking of science as a career, said P. Kay Lund, director of the division of biomedical research workers at the National Institutes of Health, perhaps the best thing would be for a mentor to sit down with them and have a heart-to-heart talk, preferably when they’re still undergraduates.”

I posted this on the CSUPERB Facebook page and a follower responded, “I am starting my PhD in September. Looks like I better focus on industry when I graduate.”  I was glad to see the resulting discussion. I am not sure Facebook comments count as the “heart-to-heart talk” Dr. Lund recommends – but we’re doing our best to raise students’ awareness of career path options (HT to Dr. Kelber* at CSU Northridge for jumping into the fray!).

Of course here at CSUPERB we’re interested in finding out where the undergraduate and graduate students we support go next in their careers.** We want to know whether the education they received in the classroom and working alongside CSU faculty mentors prepared them to be ‘life-long learners’ and creative problem-solvers capable of contributing throughout society.

Last year at annual reporting time we made our first attempt to reach out to Howell and Presidents’ Commission Scholar alumni.  This year*** we mined final reports, surveyed graduates, and followed up with about 700 undergraduate and graduate students we supported over the last handful of years. I can’t resist sharing our first cut at the data (thus the screen-shot quality of the figure!). Amazingly only 16% of the CSUPERB-supported students are lost to the sands of time and faculty lab websites (we loved great examples like this, this and this!); we were able to determine the remainder graduated, completed their degree programs or continue in their studies on CSU campuses.

Our “CSUPERB alumni” are doing great things and working in fascinating organizations nationwide.  The word cloud at the top of the post adds some flavor to these rolled-up data (the bigger the font size, the more CSU alumni are working or studying in that organization****). About 32% of CSUPERB-supported student researchers entered graduate school (this figure mixes undergraduate and graduate student outcomes; see slightly larger figure here). The majority (58%) have degree-relevant positions in biotech companies, universities, hospitals, government laboratories and non-profit research settings.  Most are still hands-on scientists, clinicians and engineers working in research, production and design facilities.  Some of the alumni who have been working for a while (> 3 years) are working their way into management roles, gaining regulatory expertise and even starting companies.  About 10% are employed in a field unrelated to biotechnology. By including CSU I-Corps alumni, we see business students don’t always continue on in the life science industry – but some do!

We’ll talk more about this data at the summer Faculty Consensus Group meeting Monday, August 1st. I’m looking forward to the discussion with CSUPERB’s committed and effective faculty mentors!

2016Graduates_Outcomes

 

 

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*Dr. Kelber noted the NY Times article didn’t “cite any employability stats for those with PhDs vs others (it only states that most PhDs were employable).”  Some graduate schools are starting to track graduates’ career paths and even publicize the outcomes. For instance, UC San Francisco (UCSF) posted their 2012 data on a website (https://graduate.ucsf.edu/basic-sciences-career-outcomes). The NIH, NSF and others are also improving their data collection methods, aiming to better track career outcomes for doctoral level researchers.

**There’s a new level of controversy about linking career outcomes with higher education. It is extraordinarily inexact to try linking life outcomes to a set of genes; likewise it’s difficult to predict career outcomes on a combination of courses and co-curricular activities like undergraduate research.  So – I’ll use the classic “SEC-type disclaimer” here; our data are not “forward-looking,” it’s based on past student cohorts and can’t be used to predict individual outcomes!

***We did this work with the very capable help of our CSU STEM VISTA Summer Associates, Ms. Zarate and Ms. Stelter!  They investigated “last known status” of ~700 students supported on CSUPERB Major Grants (2011 – present), Howell Scholars (2007 – present), Presidents’ Commission Scholars (2011 – present), Student Travel Grants (2011 – present) and I2P/CSU I-Corps participants (2012 – present).

****Yes – it appears that CSUPERB-supported alumni seem to beat a wide path to UCSF…

Word cloud image credit: http://www.wordclouds.com/

    Spring 2016 Grant Program Report: Success Rate Declines

    Yesterday evening we sent out award letters for the New Investigator, Joint Venture and Research Development grant programs.The award list will post at our website soon, if it’s not there already.

    We’re still busy in the program office with the myriad communications and logistical details of giving out CSUPERB grants. We have yet to announce Curriculum Development, Travel, Presidents’ Commission grant awards – so hold tight out there; we’ll get them made before the fiscal year close.  I want to take a break, though, and let you know about our new funding rates.  Spoiler: they’ve declined.

    All CSUPERB grant and award programs are competitive and involve peer review panels of CSU faculty. We make funding decisions based on 1) recommendations from the CSU faculty proposal review committees, 2) the available CSUPERB budget, and 3) program priorities.  We get ranked order lists from review panels.  We “pay” down that list as long as we have funds to make grants; this year we have a ~$510,000 budget to make major grants.  The Faculty Consensus Group and Strategic Planning Council set “program priorities” each summer and they are reflected in the requests for proposals (RFPs) we issue each fall. In addition the FCG and SPC want to see similar funding rates across all grant programs, if possible. There is no CSUPERB ‘formula’ for campus or disciplinary distribution of funds. The awards made depend on applications received.

    CSUPERB calculates “success” or “funding” rates as (the number of awards made) divided by (the number of applications received); we usually report these rates as percentages.

    Due to the increase in applications this year across programs, we’re making awards to only 26% of the applicants, down from our average “success rate” of 33%.  This year we saw a large spike in the number of applications to the New Investigator and Curriculum Development programs; across grant programs we’ve received 25% more applications this year compared to last year.

    Interestingly 77% of the New Investigator applicants were first-time applicants to CSUPERB major grant programs, reflecting new hiring system-wide. We’re making awards to new faculty members in biological sciences, chemistry and biochemistry, bioengineering, physics, geology and kinesiology departments system-wide.  They are investigating new coatings for drug-eluting stents, point-of-care diagnostic devices, biosensors, small molecule inhibitors of viral infection, genomic effects of environmental toxins, fundamental mechanisms of cell development, the role of alternative splicing in adaptive evolution and more. Just think of the cool science and engineering projects CSU students will be part of in the coming years!

    This funding rate is sad news for faculty applicants who might have been funded at the higher funding rates (we publish those rates in our annual report).  We follow national reports and news about peer review, of course.  We know that the difference between proposals at the 25% and 30% “pay lines” are negligible and is not predictive of future success or impact.  Many disappointed applicants are going to receive the written reviews and wonder why they weren’t funded based on the positive and encouraging things they read there (we’ll send written reviews to applicants later this week).

    We hope the written reviews will help PIs focus on points to be made when writing proposals to NSF, NIH and other external-to-the-CSU funding agencies. Each year I get emails saying ‘CSUPERB didn’t fund me – but NSF did!’ I celebrate those moments too. Each new research grant represents uncharted discovery opportunities for the CSU’s students.

    What I advise between now and next February’s proposal deadline is to: 1) call the CSUPERB program office for advice and pointers (we run a proposal writing workshop* at each CSU Biotechnology Symposium), 2) sit down with a colleague who has won CSUPERB funding to get tips and advice, 3) write a new draft (far in advance of the next deadline!) for a general review panel – not a panel of experts in your subspecialty (!) and 4) have someone else willing to read it, able to red-line edit like crazy, and who is not an expert in your subspecialty. Last – but definitely not least – address ALL the CSUPERB review criteria in your proposal. It’s not only about the science or technology at CSUPERB. It’s also about demonstrated need, future plans, student involvement and/or partnerships (depending on what RFP you’re answering!).

    Grantsmanship requires life-long learning. Sometimes it can feel like there is never enough time to learn when you’re teaching multiple sections of organic chemistry, working with a student researcher on a lab protocol, writing proposals, serving on committees, and trying to move a research idea forward. But – pace yourself – take the time to read a lot, follow Twitter feeds from experts in your field, get advice from colleagues, find a mentor to help, stay grounded in why you chose this career, and rest. In academia there is always another deadline ahead.

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    *Find here a slide deck from our January 2016 CSUPERB proposal writing workshop. It’s dated – assume details reported here will be different for the next review cycle!

      Guest Blog: José C. B. Bezerra

      From the Editor: This is a guest blog written by Dr. José Clecildo Barreto “Barret” Bezerra, a visiting professor from the Federal University of Goias (UFG) in Brazil.  He won a 6-month fellowship from a Brazilian government agency, Coordination for the Improvement of Higher Education Personnel (CAPES), to study how CSUPERB works with our regional and university partners to offer biotechnology entrepreneurship education across California. Barret arrived at CSUPERB right before the annual CSU Biotechnology Symposium and jumped right in, serving as a behind-the-scenes photographer during CSU I-Corps activities that week in January. As a result – I had a hard time finding a photo of him in our archives (below!).  He hopes to improve his english speaking and writing skills while he is here, so he’s taking classes and immersing himself in the entrepreneurship and innovation ecosystem here in San Diego. I was delighted he agreed to my challenge to write a blog post! We’ve only lightly edited this blog post since we know our readers will understand the very steep learning curve Dr. Barret’s on here at CSUPERB.  The similarities and contrasts between the US and Brazilian biotechnology ecosystems fascinate us. It’s been very interesting to all of us in the office having him here – we hope you’ll learn something about how other countries encourage a “greater proximity between knowledge and market” as well.


      The California State University (CSU) Program for Education and Research in Biotechnology (CSUPERB) has a mission to support and improve the biotechnology workforce into California. The program reinforces interdisciplinary characteristics that are fundamental and indispensable to university biotechnology discovery. But CSUPERB also balances the demand for professionals with the skills needed in today’s workforce whether graduates enter the life science industry or stay in universities.

      The fellowship proposal I wrote was inspired by Creative Innovation and Education Overseas. I submitted it to the Brazilian agency, Coordination for the Improvement of Higher Education Personnel (CAPES). I proposed studying how CSUPERB works across the State of California since it is organized to serve the CSU’s biotechnology students and faculty researchers at all 23 campuses. By bringing together researchers from a variety of disciplines, CSUPERB promotes interdisciplinary learning, as well as research-based discoveries and innovation. I was fortunate enough to win this fellowship and as a result, since December 2015, I have been based in the CSUPERB program office to study research-based innovation with the purpose to add high education, technology transfer system and a management of interaction with innovation environments to Brazil’s models.

      Brazil’s universities are growing their international reputation in terms of world-class research and innovation as investments in our universities from federal funding agencies, such as National Council for Scientific and Technological Development (CNPq), Brazilian Innovation Agency (FINEP) & CAPES. In addition, supports from the Brazilian States’ Foundations for Research Support have also increased. Brazil is building a policy framework to make efficient investments in strategically-important business sectors (sectoral funds), especially high technology sectors for which the government would like to see greater proximity between knowledge and market.

      In January 2016 Brazil took another step forward with the adoption of a new legal framework for Science, Technology and Innovation. A new law was adopted by National Congress (n. 13.243) to stimulate scientific and technological development. Among the various topics of this law, it includes provisions for monetary incentives (royalties) to universities and researchers engaging in innovation activities. Among various guidelines and goals, the law supports the development of human resources (students, administrative staff and faculties). The new law asks higher education institutions to establish technology transfer and innovation policy processes.

      Since my arrival in San Diego, I have learned that CSUPERB is already running programs and following strategies that are aligned with our new Brazilian legal decision. I think that well-structured and institutionally supported educational programs in strategically-important research sectors (for example, biotechnology) can boost the achievement of goals that the new Brazilian law aims to reach. What I have observed so far is that CSUPERB has decided to put students at the center of its programs, and I think the program is highly effective because students are included in research and development (R&D).

      Countries have biotechnology, in large part, organized in the form of innovation habitats. Biotechnology “integrators”, like regional initiatives, research centers and industry associations, help build bridges between knowledge and practice leading to technological transfer. These bridging initiatives are considered to be one of the key elements for sustainable scientific infrastructure, for example: the United Kingdom’s One Nucleus (onenucleus.com), Singapore’s Biopolis (Fischer & Mellon, 2013), Germany’s Biotecnological Cluster in Germany (http://www.clib2021.de), and California Life Sciences Institute’s FAST program. Governments and industry are making large investments in biological resources, but a number of institutional and interdisciplinary research programs also integrate career planning and student professional development, which should be intensified.

      An example in the United States is the ongoing National Science Foundation program called Innovation Corps (I-Corps™). It is a nation-wide program that encourages research-based innovation and entrepreneurship. I-Corps provides a experiential learning opportunity for students and faculty and involves industry mentors, redrawing the usual university- or faculty-based mode of mentoring. We all know that mentoring is important in developing research and laboratory skills, in classroom-based learning, but I-Corps extends mentoring into innovation. I-Corps mentoring also fosters the professional development of faculty researchers and principal investigators by teaching them about product markets (scientific or technological). As a result, they understand better how technology transfer happens and even how they might contribute to workforce development.

      CSUPERB runs one of the NSF’s I-Corps Site programs, CSU I-Corps. Altogether, what I have observed so far is an evolution of new educational practices. CSU I-Corps is awakening in faculty mentors and participating students the desire for off-campus activities. Quite often, teams are motivated to address social or public health problems that might be solved by some kind of research-based solution. CSU I-Corps encourages researchers to find “problem-solution fits” (Osterwalder et al. 2014, page 49). I-Corps activities teach researchers that there is not only a commercial point of view, or to solely expand skills, but that there also is an objective to search for viable solutions to improve the quality of life and build a qualified workforce. CSU I-Corps does not directly prioritize the opening of a new businesses or increased income, goals that incubators and technological parks often target, but instead I-Corps encourages teams to learn about knowledge transfer and commercialization strategies.

      I have also seen that CSUPERB encourages interdisciplinary collaboration (engineering, biomedical, applied social sciences and even business administration) to involve the 23 CSU campuses and encourage students and professors to conduct biotechnology research. Along with over 650 others, I attended the 28th Annual CSU Biotechnology Symposium in Orange County on January 5-7, 2016. This annual event highlights the role of the university as a producer of new knowledge and graduates in strategic business sectors, such as biotechnology. The symposium also emphasizes that the tight association of teaching practice, research and application should be highly valued. CSUPERB operates through a network of key faculty members. After the symposium, dozens of faculty members on CSUPERB’s Faculty Consenses Group (FCG) participated in a meeting that made plans and designed the best practices for the program based on CSUPERB’s strategic plan and input from faculty at 22 of the 23 CSU campuses. I think that program transparency and clear objectives can provide a trusted framework for innovation.

      We should encourage curiosity and creativity in all our students, and for that reason, some faculty mentors attending the symposium learned how to be more skillful and strategic in the development of students. I attended the “Culturally Competent Mentoring” workshop at the symposium and learned about training with inclusive approaches and appropriate care. I also learned that faculty members can be strategic leaders and, at the same time, create environments in which creativity, innovation and teamwork happen around the student. This workshop showed me the close correlation between teaching and research – and the impact that a program like CSUPERB can have.

      Brazil’s new approach to innovation (National Congress Law Nº 13.243/2016) aims to strengthen and integrate the links between university knowledge and the world of work. Similar to California, Brazilian biotechnology research also contributes to advances in new markets and prioritizes government investment in this strategic sector. However, our major universities and research centers have difficulty finding an introductory market strategy for their discoveries or new products, just as our American colleagues do (OECD, 2010; 2015). Programs like CSUPERB end up supporting bolder policies of technology transfer, expanding the participation of faculty researchers in new ventures and innovation, and building awareness of the commercialization process among students. Of course, our students are full of innovative ideas and – in the future – they will likely be collaborators, research partners or owners of the next generation of biotechnology businesses.

      References

      Blank, S. (2012) Innovation Corps: A Review of a New National Science Foundation Program to Leverage Research Investments. Available online: http://democrats.science.house.gov/sites/democrats.science.house.gov/files/documents/Blank%20Testimony.pdf

      Brazil (2016) Science, Technology and Innovation. Law Nº 13.243, January 11th DE 2016. Available online: http://www.planalto.gov.br/ccivil_03/_Ato2015-2018/2016/Lei/L13243.htm

      Fischer, M.M.J. & Mellon A. W. (2013) Biopolis: Asian Science in the Global Circuitry. Science Technology Society, 18(3): 379-404. Available online: http://sts.sagepub.com/content/18/3/379.abstract

      OECD (2010) Innovation to strengthen growth and address global and social challenges. Available online: http://www.oecd.org/sti/45326349.pdf

      OECD Innovation Strategy (2015) An Agenda for Policy Action. Available online: http://www.oecd.org/sti/OECD-Innovation-Strategy-2015-CMIN2015-7.pdf

      Osterwalder, A., Pigneur, Y., Bernarda, G., Smith, A., Papadakos, T. (2014) Value Proposition Design: How to Create Products and Services Customers Want. 320 pages. Published by John Wiley & Sons, Inc., Hoboken, New Jersey. (2015 Thinkers50 Strategy Award)

      About the author: Dr. José Clecildo Barreto Bezerra, Professor of Federal University of Goias (UFG) in Brazil and Doctor in Natural Sciences from the University of Hamburg, Germany, is on sabbatical at SDSU/CSUPERB with Dr. Susan Baxter’s guidance. His special interests here are researching learning-teaching methodologies and the interaction between universities and enterprises. In Brazil he teaches special classes: “Innovation Management, Entrepreneurship and Opportunities” and “Management and Entrepreneurship in Biotechnology.”

      barretDec2015

      Ed. Note: Dr. Barret attended all the CSU I-Corps sessions at the 28th Annual CSU Biotechnology Symposium – but this was one of very few he was in front of the camera, albeit way in the very back (blue arrow!)

       

        Workshop Report: Preparing Students in Bioinformatics

        Bioinformatics7I’m pleased to turn the CSUPERB blog over to Bori Mazzag (Humboldt State University) and Sandra Sharp (CSU Los Angeles)!  Bori and Sandy are both members of the CSUPERB Strategic Planning Council.  They jointly organized the “Preparing Students in Bioinformatics: Challenges, successes and opportunities” workshop held January 8, 2016, during the 28th annual CSU Biotechnology Symposium at the Hyatt Regency Orange County. Here is their workshop report:


        This year for the first time, the CSUPERB GATC (Genomic Analysis and Technology Committee) and the QB (Quantitative Biology) faculty networks hosted a joint workshop at the 2016 CSU Biotechnology Symposium, entitled “Preparing Students in Bioinformatics: Challenges, successes and opportunities.” The two groups are led by Sandy Sharp (CSU Los Angeles, CSULA) and Bori Mazzag (Humboldt State University), respectively.

        The GATC has focused on research-based curriculum since its inception in 2010. QB has worked on exploring and disseminating best practices in quantitative (mathematical, statistical and computational) preparation of CSU biology students. The two interest groups have organized separate sessions at the CSUPERB Symposium since 2012, but with members of each group expressing a desire for a workshop on bioinformatics, we decided to undertake a combined offering. It turned out to be a powerful, well-received strategy!

        We concentrated on two main themes: (1) Does the current bioinformatics training offered by CSU campuses meet workforce needs? (2) What are some differences between the skills needed by end users/biologists versus programmers/software developers?

        To address these questions, we invited a panel of CSU faculty, industry employers and hiring managers: Jamil Momand (Chemistry and Biochemistry, CSULA) and Nancy Warter-Perez (Electric and Computer Engineering, CSULA), Paul Wolber (Agilent and San José State University, SJSU), Soheil Shams (BioDiscovery, Inc.), and Pleuni Pennings (Biology, San Francisco State University, SFSU).

        The "Preparing Students in Bioinformatics" workshop featured a "bi-directional" panel of CSU faculty, industry employers and hiring managers. The panelists were (left to right): Paul Wolber (Agilent and San José State University), Soheil Shams (BioDiscovery, Inc.), Pleuni Pennings (Biology, San Francisco State University, Nancy Warter-Perez (Electric and Computer Engineering, CSU Los Angeles) and Jamil Momand (Chemistry and Biochemistry, CSU Los Angeles).

        The “Preparing Students in Bioinformatics” workshop featured a “bi-directional” panel of CSU faculty, industry professionals and hiring managers. The panelists were (left to right): Paul Wolber (Agilent and San José State University), Soheil Shams (BioDiscovery, Inc.), Pleuni Pennings (Biology, San Francisco State University), Nancy Warter-Perez (Electric and Computer Engineering, CSU Los Angeles) and Jamil Momand (Chemistry and Biochemistry, CSU Los Angeles).

        The ~45 workshop attendees included faculty members from 18 of the 23 CSU campuses and 4 California Community Colleges. Faculty from a wide range of disciplines participated, from Biology, Chemistry and several different types of Engineering. Participating faculty members either aspire to or are already involved in bringing bioinformatics into the classroom, often as components of original student research. The workshop facilitated the sharing of expertise and challenges in genomics/informatics research and teaching, with the aim of providing the best possible learning experiences and outcomes for our students.

        The workshop began a panel discussion, followed by round-table discussions among the participants, with panelists and other faculty participants serving as discussion leaders. Near the close of the session, each table shared a few important lessons learned. Workshop participants who had curricular materials to share also spoke briefly about their work and the materials they were offering.

        First, each panelist described his or her training and current work in genomics/informatics research and education. It was fascinating, and even somewhat surprising, to realize that each panelist arrived at their current position by career paths that required them to cross disciplinary or sector boundaries. For example, Paul had long been working at Agilent when he became an external evaluator and advisor for the SJSU bioinformatics program. The collaboration grew, and Paul has now been teaching an engineering course on next-generation (“next-gen”) sequencing technologies at SJSU for several years. He also described positive impacts his teaching job had on his own industry career.

        Drs. Warter-Perez and Momand describe a biology-computer science course they co-taught. Bori Mazzag (Humboldt State) moderated the panel discussion.

        Drs. Warter-Perez (left) and Momand (center) describe a biology-computer science course they co-taught. Bori Mazzag (right, Humboldt State) moderated the panel discussion.

        Jamil and Nancy gave a detailed description of the bioinformatics course they team-teach to computer science and biology students. They shared strategies and philosophies around designing a successful course that meets students at their current level, but also pushes them to complete an interdisciplinary project. As instructors from very different backgrounds, they model the sort of interdisciplinary collaboration they ask from their students in the course.

        Soheil talked at length about the need for programmers at his company and the pressures his and other, similar mid- and small-sized bioinformatics companies feel in competing with the likes of Google or Uber for software engineers. From his perspective, one of the greatest challenges is to inspire (or recruit) and train (and retain) programmers who are willing to forego some potential earnings to work on and solve the new and impactful problems that biology has to offer.

        Pleuni shared information about her own training that built on a biology background but became increasing quantitative. The bioinformatics course she developed draws upon that experience.Bioinformatics6

        The academic panelists spoke on skills or knowledge they want to impart to students and what challenges they face as instructors with students varied levels of preparation. Industry representatives talked about important skills needed by programmers and end users, but seen as lacking in current job candidates. Not surprisingly, both written and oral communication were mentioned as a critical skill for all students entering the job market. Several examples were given of the specific types of writing required and it was clear from Paul and Soheil’s comments that although writing is more emphasized in teaching STEM fields nowadays, there is a need for continued improvement in this area.

        A discussion developed around the term “bioinformatics” itself. Soheil argued that it is too broad an umbrella term that encompasses vastly different types of jobs and skills.* This point resonated with many in the audience and came up as an important takeaway in the post-workshop survey. As Bioinformatics2it often happens in interdisciplinary settings, the panelists and audience were split on the relative importance of increasing depth of knowledge in a discipline versus interdisciplinary training. Often those who advocate for depth see interdisciplinary projects primarily as a way to teach students how to communicate and work with others from a different discipline. Others see interdisciplinary training as a fundamental, new approach to teaching content to students. This perspective often implies that the current academic silos do not provide the right organizational structure for the sort of work that graduates do or problems they face after leaving school.

        As CSU faculty members, it was interesting to us to discover the diverse ways campuses, departments and researchers have devised to teach bioinformatics and mentor their students in this field. Because bioinformatics is so new and technologies evolve so quickly, professionals and professors in the field must stay agile. For some, it means learning new programming languages, building new collaborations around research questions, pooling resources, or sharing equipment across campuses.

        One challenge for faculty has been finding resources and a network of CSU researchers in the field, dispersed in home departments across engineering, computer science or biology. CSUPERB, and the GATC specifically, has been instrumental in facilitating networking across the CSU. Bay Area and Southern California campuses certainly benefit from having tight connections with industry (for example, the SJSU/Agilent relationship). But far-flung or isolated campuses, such as CSU Chico, have successful bioinformatics concentrations as a result of purposeful hiring and faculty networking.

        Bioinformatics4The panel discussion was followed by round-table discussions involving all participants. One table gathered faculty who all teach a bioinformatics course. The course designs described varied greatly. Much of the discussion centered on recruiting students to take bioinformatics courses (for whom programming is often a deterrent) and how to teach programming most effectively. Most agreed that for biology courses in which informatics software is used as a tool, it is necessary to treat the software itself as a “black box” to some extent, but there was disagreement over where the right limit was.

        An interesting side-note: MANY participants wrote they would like to see further workshops and training on programming, either in R or Python or other languages. CSUPERB will look into inviting Software Carpentry to offer a workshop to faculty this year.

        Janey Youngblum (CSU Stanislaus) motivates students by getting genomes sequenced by 23 and Me. This resonated with many of the participants. While there are several problematic, ethical and financial considerations around using students’ genomic data, making research questions personally engaging and relevant clearly struck a chord among the workshop participants.

        Bioinformatics5

        Amy Sprowles (Humboldt State) takes notes as Judy Brusslan (CSU Long Beach) describes CyVerse as a bioinformatics teaching and learning platform.

        Two other tables had extensive discussions about programming and software. Clearly, finding the right software to teach at the right level has been a huge obstacle to effective teaching and desired learning outcomes. As more on-line tools become available, and some methods standardize, this hurdle may become easier to cross over time. One of the most animated table discussions was on iPlant (or now CyVerse). The discussion morphed into a mini-tutorial by Judy Brusslan (CSU Long Beach) on how to use CyVerse for the analysis of large data sets. Because CyVerse has cloud-based data storage and analysis tools, many concerns about availability of computational power and storage space have been alleviated.

        Several members of the audience, including David Keller (CSU Chico), Jose de la Torre (SFSU) and Renaud Berlemont (CSU Long Beach), talked about their curricular materials and shared materials or posted links to them. We also learned that Jamil and Nancy’s book, based on their team-taught course, is going to be published this year.

        In the immediate post-workshop survey, a handful of main takeaways were mentioned. These open text replies are representative:

        • “There are (effective) strategies to teach bioinformatics to bio students without programming skills”.
        • “Next-Gen Analysis is possible at CSU.”
        • “Finding out what’s going on related to bioinformatics on other campuses.”
        • “Learning about different resources to use in my courses.”
        • “Lots of cool resources and programs at different institutions.”

        The session also received very positive feedback from faculty participants who responded to the post-symposium survey. We have been in contact with the workshop attendees, disseminating workshop notes, contact information and curricular materials. There is a lot of energy around bioinformatics (for lack of a better term!) networking and developing a workshop around hands-on skills (perhaps programming!) next year.

        — Bori Mazzag & Sandy Sharp


        *Editor’s note: A recent search of bioinformatics-related corporate (non-academic) job position openings in California (Jan. 2016) used these technical keywords: statistics, data analysis, data management, quality control, version/revision control, software engineering, methods development, algorithm development, expertise in a series of scripting languages (“Perl or Python, R, shell scripting, and MySQL”), programming skills in a series of languages (“Python or Perl/Java/C++; shell scripting and R”). Many job descriptions dedicate more text to “soft skills” (communication, agility, teamwork, etc.) than technical skills.

          CSUPERB-supported students – who are they?

          Each year CSUPERB organizes and hosts the annual CSU Biotechnology Symposium. The 28th annual event January 5-7, 2016, brought together 403 student researchers from 21 of the 23 CSU campuses.*

          The post-symposium surveying is now complete.  96.4% of students responding (28.5% of those who attended) would recommend it to other students. 100% of faculty responding (40% of those who attended) would recommend the meeting to students or other faculty.

          These endorsements are a real testimony to the Faculty Consensus Group (FCG) members (if you follow that link you might want to hit play and mute your computer!) who put significant thought, work and creativity into this year’s program.  We also – of course – had a small army of invited speakers, industry mentors and evaluators who brought their perspectives, stories and verve to the meeting.  It’s amazing to see all the moving parts come together each January. This was my 9th symposium. The fall ramp-up to the symposium is draining from a small office organizational viewpoint – but I can tell you the CSUPERB program office floats through the year on the energy and goodwill we harvest during the symposium!

          CSUPERB and our sponsors subsidize the cost of symposium participation for CSU students.  Each year as they register, we ask students for information about themselves so that we can track the make-up of the students we support. I’m a sucker for free web-based software so I graphed out student responses using Piktochart this year (see below – or surf to the dynamic version on the web: https://magic.piktochart.com/output/11020572-csuperb-supported-students).  I can’t tell you how many times during the year I use this data for grant proposals and presentations outside the CSU – so I wanted to share this data with the CSUPERB community. We’ve been tracking this dataset for 3 years now; this year’s responses are not significantly different than previous years’ data.

          It’s policy report season so I’ve recently read lots of thought-provoking and sometimes frustrating higher education, workforce development and research-related monographs. However, one worth discussing here is a new (prepublication) report out of the National Academies Press (NAP) titled, “Promising Practices for Strengthening the Regional STEM Workforce Development Ecosystem.” (Free PDF available at www.nap.edu/21894). It leans heavily on National Science Board (NSB) data found in the 2014 “Revisiting the STEM Workforce” report.

          As readers of this blog know well – I’ve often railed against general calls for more STEM graduates.  The NAP and NSB reports do a great job describing the “heterogeneity of the STEM workforce and lack of consensus on how to define it…” However the reports (rightly IMHO) offer data and citations that focus on “high level of attrition, especially of women and underrepresented groups, among students in STEM majors.”  That’s why I’m so proud to share our data on the student researchers and entrepreneurs who presented at the 28th CSU Biotechnology Symposium.

          The recommendations outlined in the NAP report map surprisingly well to the strategies adopted by CSUPERB these past 8 years or so. The annual CSU Biotechnology Symposium itself is a classic example of a “larger-scale, convening event” called for in the report!  The NAP report lists promising practices, including:

          • “More hands-on, project-based learning activities for students.
          • Professional development for teachers in project-based learning instruction.
          • More opportunities for students, teachers, and parents to interact with STEM professionals and learn about employers and career opportunities.
          • Outreach to females and underrepresented minorities that includes opportunities to meet role models and mentors who look like the students. 
          • Mechanisms to facilitate connections between teachers and STEM professionals who wish to function as volunteer speakers and/or mentors.”

          The annual symposium program incorporates these promising practices, including the opportunity to showcase the high level of “hands-on, project-based” research and entrepreneurial projects the CSU’s students produce.  The 264 posters and 13 CSU I-Corps team presentations represent faculty-student research supported by NSF, NIH, HHMI and other national funding organizations. While none of the CSU campuses are classified as Research 1 universities, the hands-on, project-based learning opportunities mentored by CSU faculty systemwide are of outstanding quality and have tremendous impact on the career trajectories of our students.**

          The educators, industry professionals, sponsors and policy leaders who come to the symposium “recognize the importance of strong college-university-industry collaboration in preparing the STEM workforce of the future.” CSUPERB works with “intermediary organizations,” like BIOCOM and California Life Sciences Institute, who understand the bi-directional partnerships needed to nurture a healthy biotechnology industry ecosystem. Doctoral program representatives and community college colleagues join us at the event to build bridges and pathways for our students and theirs.  We thank Gilead Sciences, Inc., Agilent Technologies, BioDiscovery, CourseKey, Grifols Biologicals, Inc., Rare Science, Inc., Slater Hersey and Virun for their financial support – but also their employees who were a vital part of the 28th annual CSU Biotechnology Symposium.  The National Science Foundation provided funding for the CSU I-Corps program – a very popular, new part of the symposium program. These relationships and ongoing partnerships are the basis on which CSUPERB carries out its strategic goals; the annual symposium is the “convening event” that brings us together again face-to-face (even in nano-second drive-bys!).

          The real reason we all keep coming back to the annual CSU Biotechnology Symposium is to meet the students who come to the symposium each year. Having 9 symposia under my belt now, my LinkedIn network is beginning to swell with CSU alumni working in the biotechnology industry. This year many of them came back to the symposium as mentors and speakers.  I can’t tell you how rewarding it is to see them again, hear their stories and watch them give back to the current students attending the symposium. Join us next year – it’s a great event!


          *See three symposium-related photo galleries on the CSUPERB Facebook page: (1) Speakers, Career Networking Session and more, (2) The Eden & Nagel Symposium Award programs and (3) CSU I-Corps

          **For student impacts, see here and here. Most CSU faculty in biotechnology-related departments earned their PhDs and spent postdocs at R1 universities in the US and they do world-class research!  Browse this year’s poster abstracts for a flavor of the biotechnology research going on across the CSU.

          csuperb-supported-students (2)

            New CSUPERB Annual Report – bigger and full of news

            CIRM issued its new Bridges 2.0 Request for Proposals in August.  In answer CSUPERB scrambled to organize two proposal writing workshops for interested campus proposal writing teams.  We figured it was worth delaying our annual reporting to make sure campus teams had the information they needed to respond to CIRM’s new program requirements; there are millions of training grant dollars at stake!  Many thanks to Dr. Michael Yaffe (CIRM) for spending afternoons at Cal Poly Pomona and San Jose State University explaining the new program requirements. Bridges 2.0 proposals are due tomorrow; good luck to all the applicant campuses and their partners.

            The poster abstract deadline for the 28th Annual CSU Biotechnology Symposium was this past Monday.  Tyson Gadd is still culling through the submissions, removing duplicates and checking for completeness, but it looks like the poster abstract selection committee has their work cut out for them again this year; we predict we will only be able to accept 75-80% of the abstracts submitted. The preliminary count suggests there are over 20 Eden Graduate Research Award nominations and 13 Nagel Undergraduate Research Award nominations. Because we can only accommodate a limited number of award talk presentations in the symposium program, the award selection committees must narrow the Eden and Nagel fields by naming finalists in these highly competitive system-wide award programs.  Finalists and authors on selected posters will receive email notifications from CSUPERB the first week in November.

            PosterGroup_2424

            So this month as the fall academic term began in earnest, research teams wrote abstracts, and Bridges 2.0 teams did the hard work of building partnerships, CSUPERB finished up our AY 2014-15 Annual Report (linked here).  We figure most people read the electronic version of the report these days.  This year we concluded our previous efforts to keep the report’s page length short meant we were using ridiculously small font sizes and leaving out some of the best news from CSUPERB’s PI and student researcher community.  So this year’s annual report has grown from six pages to ten!

            As always the annual report features some wonderful, follow-on outcomes from our seed grants. Each year our supported researchers – students and faculty – write graceful, reflective and thoughtful final reports.  As we read through the final reports, it is clear that the “extracurricular,” high-impact practices, partnerships and creative projects we fund open doors, opportunities, and paths that transform careers, departments and campuses at both the student and faculty levels.  We are so glad we have the ability to “put our toe on the gas” of these career and research program trajectories; we are proud of what these researchers have accomplished!

              Guest Blog: Paula Fischhaber Teaches in China

              The CSU’s biotechnology faculty are remarkable educators with wide-ranging research interests and partnerships both on and off-campus. CSUPERB continues to focus on building partnerships as part of our professional development programs, but many (most?) research-active CSU faculty already have wonderful research collaborations and external partnerships worldwide, as you’ll see!  The beneficiaries of successful and collaborative research partnerships? Students, of course! Faculty who collaborate with external groups bring not only cutting-edge science and technology into their CSU classrooms and labs, but also new perspectives to their teaching and mentoring.

              Occasionally someone will tell me a great story and I ask them for a “guest blog post.” As regular readers can tell, our busy faculty don’t take me up on the offer very often!  But – Paula Fischhaber (Associate Professor in the Department of Chemistry and Biochemistry at California State University Northridge & member of CSUPERB’s Strategic Planning Council) did so despite a crazy, start-of-semester schedule!

              Paula-Great WallPaula traveled to Beijing this July to teach a one-week Biochemistry course at Capital Normal University (CNU), a relatively small university (~20,000-25,000 students) in China. That’s Paula on the Mutianyu section of the Great Wall of China in the photo on the right.  Here are her reflections on the experience:*


              My class constituted 20 hours of instruction with 2-hour sessions held morning and afternoon each day. Most of the students in my course were senior Biology majors who had taken Biochemistry the previous year, taught in Chinese. Many Capital Normal University (CNU) students aspire to enter the teaching profession in the K-12 age range. Others plan to pursue Ph.D. degrees following graduation, so I got lots of questions about applying to doctoral programs in the United States. One student was even planning to take part in a summer program at UCLA within a few weeks of my return home.

              Class PhotoI was first struck by how the demeanor of the students (photo above) was so similar to those at Cal State Northridge. There were some who were more outgoing and eager, others that were shy or timid about speaking in English. Some were highly advanced, both in their English language skills and their understanding of biochemistry. Some were so afraid of me that they would scarcely make eye contact. As the week wore on, the ice broke and they asked increasing numbers of questions, especially during the afternoon interactive problem-solving sessions (yes, flipping the classroom has its advantages universally). The students were ALL very respectful toward me, and several brought food items to share that represented Beijing specialties that I was not to leave town without trying.

              One particular student was soft-spoken and shy-ish but had an eagerness about the material that was contagious for the other students. He asked many questions throughout the week and I could see was not just improving his English, but also his understanding of the biochemistry, which was gratifying for me. On the last day of class, I called on him to explain the last figure of a paper and (being shy about his English) was shaking a little as he reached for the words, which he did successfully.

              At the end of the class when I was saying my good-byes, he came up to me to say that all the students had learned a lot from me and they were grateful for the class and would miss me. As he waved and left the room, I realized that he might have had to summon courage and to practice his remarks ahead of time. Those are the moments in a professor’s life that make it all worthwhile, but it reminded me that Cal State Northridge students are also often intimidated by their professors and must summon courage to ask a question or come to office hours.

              Paula_CaiXia_BGIDr. CaiXia Guo, at the Beijing Genomics Institute, recommended me to the summer course director to teach the short course. CaiXia and I worked together in my postdoc lab group and recently coauthored an invited review in Epigenetics (here we are right next to the 2008 Olympic village; the Olympic torch is in the background).

              In conversations with Chinese faculty during the week, I came to realize that we share much with the Chinese academicians in our struggles to get and maintain research funding streams in the face of fewer and fewer available grant dollars. We share their frustration with time-consuming bureaucratic barriers. Like us, the Chinese universities are facing a difficult budget climate that leaves faculty underpaid and buildings with significant deferred maintenance. What I heard over and over was how competitive everything is because they have so many people. Everyone worries about whether they will be able to get and keep a good job. Overall, I gained a new appreciation for the education and research system in the U.S.

              ____________________________

              *Lightly edited for style and clarity.