Naturally Obsessed: the making of a scientist is a documentary by Richard Rifkind and Carole Rifkind
Mixing humor with heartbreak, the film tells a profoundly real yet intensely dramatic story about life in a molecular biology lab. “I want the viewer to stand in the shoes of a scientist at work in a lab, glimpse the world of research as it really is, and understand what it takes to fill an ample pipeline of future scientists,” says scientist turned filmmaker, Sloan-Kettering Institute Chairman Emeritus, Richard Rifkind.
(via Misha Angrist)
By Hsien-Hsien Lei, PhD, HUGO Matters Editor
At a meeting with HUGO President Prof. Edison Liu on Monday, we talked about the tremendous opportunities for utilizing personal genome data if we weren’t limited by the lack of computing power. Just last month, the DOE Joint Genome Institute held an invitation-only workshop to discuss the use of high performance computing for analyzing and managing data from genome sequencing. As sequencing becomes more efficient and cost-effective, we are reaching the next hurdle of data management, data analysis, and translational research.
One laboratory that is interested in using higher-performance computing (HPC) for genomics is the Zhulin lab at the National Institute for Computational sciences, Oak Ridge National Laboratory, University Tennessee.
The exponential growth of genomic datasets leads to a situation, where computing power becomes a critical issue. We invest in adapting powerful bioinformatics tools for use with HPC architectures. The UT-ORNL Kraken and ORNL Jaguar petascale supercomputers offer tens of thousands of processors that enable researchers to computationally analyze data on an unforeseen scale. Our first successful implementation of the HMMER software (now scalable to thousands of processors) permitted us to match every sequence in the NCBI non-redundant database (roughly 5 million protein sequences) to all Pfam domain models in less than a day.
Supercomputers used for petascale computing can perform a quadrillion (1015) calculations per second. Singapore is set to have its own cluster of supercomputers in a joint R&D partnership between Fujitsu and the Agency for Science Technology and Research.
Personal genomics company, Knome, announced the launch of KnomeDISCOVERY in November 2009. Targeting research groups, KnomeDISCOVERY will help researchers sequence DNA, manage data, and perform preliminary analyses. The service will also help clinical researchers identify novel alleles that are associated with specific diseases of interest.
Researchers with expertise in medical genomics who want to streamline data management and preliminary analysis in forthcoming mass sequencing projects - Leveraging high-volume access to sequencing platforms, Knome handles the logistical hurdles of rapid-turnaround sequencing, and carries out the important but computationally intensive process of "background" genome analysis, freeing researchers to focus on specific question-driven hypothesis testing that can yield novel discoveries in genetic medicine.
Clinically trained researchers with extensive expertise in specific diseases, for whom mass sequencing approaches are novel and unfamiliar tools – Knome’s expertise in analyzing whole genome data can directly help these researchers pinpoint novel alleles that contribute to a disease of interest. Knome takes a "fine-toothed" approach to genomic data analysis, grounded in a thorough understanding of genome structure and function; protein biochemistry; population/evolutionary genetics; statistical analysis; and basic disease etiology, as refined by close consultation with the researcher. This approach can quickly identify potentially disease-relevant candidate alleles for researchers to consider for follow-up empirical assessment.
Now that we’re getting a handle on the technicalities of sequencing, it’s time to grapple with the challenge posed by the massive volumes of data that are being produced. Translational genomics research will enable us to better understand the biology of living organisms and holds the key to better diagnosis, treatment, and cures of the diseases that ail us.
In the next decade or two, many of us will probably have our personal genomes sequenced. As of now, however, only a few hundred people in the world have had their genomes sequenced at various degrees of coverage although some individuals may have had their genomes sequenced privately. And of these, less than 50 are publicly available including the first ten participants in the Personal Genome Project (PGP-10), an initiative of Harvard Medical School.
The latest people to have their whole genomes sequenced are five southern Africans – four Bushmen hunter-gatherers and Archbishop Desmond Tutu. The data generated from these genomes will help supplement current genomic information which primarily focus on European and East Asian populations.
From the New York Times:
African genomes are of particular interest for understanding human genetic history because they have more variation in their DNA than other populations. Everyone outside Africa is descended from a small group that left some 50,000 years ago, carrying away only a small sample of the available genetic diversity.
Although the Bushmen will most likely not be in attendance, on April 27, 2010, members of the PGP-10 will be at the Genomes Environments Traits (GET) Conference in Cambridge, MA along with James Watson. The aim of the GET Conference is to “collect everyone with a personal genome sequence on the same stage to share their experiences and discuss the important ways in which personal genomes will affect all of our lives in the coming years.”
Only 200 seats total will be sold for this conference and only 32 tickets are remaining at the initial $999 price. Proceeds from the conference will benefit the Personal Genome Project which will be enrolling 100,000 members of the public who agree to share their genome sequence and personal information to further our understanding of genetic and environmental influences on human traits and diseases.
The press release for the GET Conference is below the fold.
Wishing you could attend the HGM 2010 meeting in Montpellier, France this May but short on funds? If you’re a young scientist under the age of 40 who is involved in human genome research, you could be eligible for a HUGO Young Scientist Travel Award which covers registration fees, airfare, and accommodation. Partial awards for registration fees are also available.
Applications should consist of:
- Curriculum vitae of the applicant: this should occupy no more than one single sheet and should include a list of recent publications.
- A recommendation by their superior or lecturer / mentor indicating knowledge and support of the application.
- An abstract submission on any topic listed in the HGM 2010 programme
Have you registered for the 14th Human Genome Meeting (HGM) in May? The meeting’s main focus will be on next generation sequencing and genotyping and related computational challenges. It’s of the moment, in the moment information that you won’t want to miss and the chance to network with leaders in the field.
Some of our confirmed speakers include:
- Augustine Kong of deCODE
- Christina D. Smoke of Stanford University
- David B Goldstein of Duke University
- David Cox of Pfizer Inc.
- Edward Rubin of the Joint Genome Institute
More info to come as we get closer to the big event!
Also don’t forget about the HUGO-OECD Symposium on Genomics & Bioeconomy, a satellite meeting of HGM 2010 focusing on the impact of genomics on the world economy.
- Abdullah Daar of the University of Toronto
- Gerardo Jimenez-Sanchez of OECD
- Li Jin of Fudan University
- Stephen Scherer of The Centre for Applied Genomics
- Yoshihide Hayashizaki of RIKEN Genomic Sciences Center
Let us know in the comments if you’ll be joining us!
By Hsien-Hsien Lei, PhD, HUGO Matters Editor
In our final installment of the Scientists and Social Networking Primer series, here are 10 tips for scientists interested in getting involved with the social media scene. It’s more fun and rewarding than you can imagine! For those of you who are already active, please share your personal experiences in the comments. (Also see part 1 on blogging, part 2 on social networks, and part 3 on HUGO’s social media plans.)
1. Fill out your profile. Although it might be wise to exclude personal data, such as birth date, phone number, and address, it is important to share your personal background including a photo to foster trust and believability.
2. Be sincere and consistent. The best compliment someone can give when meeting you for the first time face-to-face is “You’re the same online as well as off.” No surprises, no hidden agendas. In this case, honesty really is the best policy.
3. Identify your goals for social networking. Are you interested in career development? Or are you interested in online social networks for personal reasons, such as to get back in touch with classmates or update family members? This will help you determine the amount of time you want to spend in social networking and where to concentrate your efforts.
4. Figure out your comfort level for sharing. Are you interested only in talking about science or are you ok with sharing personal news? It’s important to remember that anything on the Internet is recorded for posterity. Even if you think no one can find what you posted 10 years ago, there’s a good chance that someone will be able uncover it.
5. Sculpt your identity. Would you like others to view you as the go-to person for all things related to genome-wide association studies? Or maybe as the scientist with a sharp eye for the ironic side of science? Your personal brand and identity are enhanced if you keep your updates and the information you share largely on topic.
6. Don’t be afraid to be opinionated. Social networks are fun and more useful if you boldly share your viewpoint. This doesn’t mean that you should go on the attack. Thoughtful commentary is valued online even more than offline because of the noise inherent in social networks.
7. Connect with people who have shared interests. Just as in the offline world, relationships develop if there is common ground. People will help you spread your message and help you network if they are truly interested what you’re about.
8. Separate your connections into groups. On Facebook and Twitter, it’s possible to sort friends and follower into groups which will help streamline the way you keep track of the latest news and events. Grouping people will also help you determine the type of information you want to share with one group but not another.
9. Respond to comments and direct tweets or messages. No one likes to be ignored, particularly online. Building a relationship is as simple as acknowledging someone’s response to your links and posts, and it is also good Internet etiquette.
10. Stay active. It’s easy to drop off people’s radar when there is so much information online. Social networking is an investment that may only start to take off after several weeks or months of regularly posting quality, relevant content. Also, people will not immediately respond to you until they see more of you. Just like any relationship, building your online network will take time, but it is worth it.
Do you have any other tips to share?
by Hsien-Hsien Lei, PhD, HUGO Matters Editor
HUGO and Social Networks
HUGO entered the social media space in October 2009 with the creation of a blog, Facebook Fan Page, Twitter account, and LinkedIn Group. HUGO’s primary objective is to engage the scientific community in discussions about the present and future of genetics and genomics and related subjects.
Of HUGO and social networks, HUGO President Prof. Edison T. Liu says, “Communicating science in the 21st century has expanded beyond traditional paper publishing. Scientists and researchers now have the opportunity to interact with each other in many different ways. With our presence on various social networking platforms on the Web, each serving different functions, HUGO is in a position to facilitate science communication and networking on a global level.”
HUGO’s blog, Hugo Matters, is the main social media hub for the organization. Links to our various online places are featured on the blog along with widgets that display the latest activities at those websites. The blog also serves as an informal ezine (electronic magazine) where brief articles by scientists are published, such as articles on the state of scientific publishing and recent results from HUGO-led studies. Interviews with prominent HUGO members as well as other researchers active in genetics and genomics can also be found on the blog. These articles, interviews, and other features give readers a behind-the-scenes look into scientific research and insight into the concerns that are uppermost in the minds of scientific leaders. Readers also have the opportunity to interact with these thought leaders along with other readers via the open comments section following each article. In short, anyone wishing to stay up-to-date on HUGO developments and those who are keen to discuss issues concerning genetics and genomics research should visit the blog first and often.
The HUGO Facebook Fan Page serves as the HUGO community forum where Facebook members can start discussions, post links, and communicate with HUGO staff in an informal setting conveniently linked to their personal Facebook account. New information posted on the Facebook Fan Page is displayed concurrently on the members’ personal newsfeed. Photos from HUGO events are also uploaded to the Fan Page to share the experience of the events and to encourage people to attend future events. The main purpose of the Fan Page is to stimulate discussions on current events related to genomics that may not necessarily warrant a lengthier write-up on the blog but are still interesting and relevant. HUGO updates are also regularly posted on the Fan Page and link to websites where more information is available.
HUGO’s presence on Twitter was particularly important during the 2009 HUGO Symposium on Genomics and Ethics, Law and Society in Geneva, Switzerland. Highlights from the symposium were covered using live Tweets from HUGO President Edison Liu and conference speaker Linda Avey, which were well received. Through the viral spread of retweets, a number of scientists and others interested in the symposium were able to keep up in real time. We also provided additional background information by including links to supplementary websites from tweets using the official HUGO Twitter account. In 2010, the HUGO Twitter account will also provide some behind-the-scenes looks into an average day in the life of a scientist, including that of HUGO President Liu. He will be live tweeting his thoughts and activities throughout one specific day and responding to any questions or comments directed at him on Twitter. HUGO also uses Twitter for rapid, almost instantaneous exchanges of ideas and information with scientists and other organisations focused on genetics research with less of the social chatter that’s found on Facebook.
HUGO’s LinkedIn Group will be developed into a career development resource for genetics and genomics researchers. Plans are still being defined but may include job postings, career advice, potential collaborations, and business development. Because of its international user base, LinkedIn is a good place for fostering cross-border support for scientists and others working in the field. It is also a place where students can learn more about careers in genetics.
Over the course of this decade, new social networking platforms will surely be developed including ones that are designed especially for the scientific community. Although it will require a significant investment of time and effort, HUGO’s commitment to social media demonstrates our sincere desire to learn directly from the international genetics and genomics research community as to how we can best serve their needs. The interests of students, post-docs, junior scientists, and senior scientists in academia and the private sector will differ in many ways. Instead of having only limited contact with supporters at annual conferences, HUGO will leverage online social networking to better connect with scientists and researchers in all countries.
The Human Genome Organisation (HUGO), one of the oldest genome organisations, is pleased to announce the re-election of Professor Edison T. Liu as its President, effective 1 February 2010 by the HUGO Council, the governing body of the organisation.
Professor Liu is the Executive director of the Genome Institute of Singapore and has been a council member and President of HUGO since 2007. Since 2007, the President under the direction of the HUGO Council has made significant changes in the organisation. Membership rules were restructured, web and social networking for the organisation established. A new journal, the HUGO Journal has been initiated with Springer Publishing Group, and the symposia schedule enhanced. More recent collaborations with the WHO, the Archon X Prize, and the OECD have extended HUGO’s participation in global policy making.
Professor Liu says: “I am honored and rather humbled at being asked to continue my role in HUGO for another term. These are unusual times for the field of genomics characterized by dramatic changes in technologies which augment the impact of our science. What excites me is that, as a professional and scientific organisation, we can make a difference in helping humanity solve some of our most serious problems in health, food, and energy. The science is strong, that the role of our individual members in their personal capacities is to push that science, but HUGO will need to guide that science through thought leadership and policy discussions. We have many challenges ahead. ”
by Hsien-Hsien Lei, PhD, HUGO Matters Editor
In the second part of the Scientists and Social Networking Primer series, we look at social networks such as Facebook, Twitter, and LinkedIn. (Also see Part 1.)
Science on Social Networks
Social networks, such as Facebook.com, Twitter.com, and LinkedIn.com can be considered an adjunct to blogging or a separate endeavor. Although not as customizable as a personal science blog, social networks also allow scientists to create profiles that demonstrate their personal and research interests as well as a way to network with other scientists. Exchanges on social networks typically occur more quickly and the discourse tends to be more succinct than blogs. In this sense, social networks mimic real face-to-face conversations with colleagues while blogs are more like online journals or magazines.
Facebook is the most popular and fastest growing social network among both general users and scientists. Users can choose to have a completely public profile or allow only accepted “friends” to view their profile and the information they share. Users can group these friends based on predetermined criteria, such as family, work, online acquaintances, and give each group different levels of access to the information that’s been posted on their profile. For example, scientists may use Facebook as a virtual bulletin board of links to the latest science news and events along with notes, status updates, photos, and videos, but allow only close personal friends and family members to view posts involving their children. Facebook friends have a News Feed on which each other’s Facebook activity is continuously updated.
In addition to interacting with one another via personal profiles and updates, Facebook users can also find others with similar interests at fan pages and groups created by individuals, corporations, or organizations, such as the HUGO fan page. Facebook fan pages and groups are virtual gathering places where the creators can connect directly with Facebook users who’ve joined. Joining a fan page or group is a good way to keep abreast of an organisation’s latest developments, offerings, and events. Facebook fan page/group notifications are more straightforward than email, are consolidated with other updates of interest from Facebook friends, and are conveniently automated.
John Fossella, assistant professor at the Mount Sinai School of Medicine, who writes Genes to Brains to Mind to Me has found social networking to be useful in many ways, “Instead of getting feedback from the same handful f folks I regularly see in the lab, I’m getting comments and new ideas from folks who I used to work with 5, 10 and even 20 years ago, not to mention new folks who I’ve struck up online-interactions with. I’ve also enjoyed social support and encouraging comments from former colleagues during times when funding and institutional-politics have been difficult to manage emotionally.”
Software applications are another feature of Facebook that add functionality to the social network. Although most involve online gaming, some are specifically about science including genetics and genomics. Sigma Life Science created the Your Favorite Gene application that can be used to find information about specific genes, create a personal list of favorite genes as well as view friends’ lists, and add publications and research interests to one’s Facebook profile. GenOmics is a community news application with featured news, top news as voted upon by members, and popular Q&A’s. The GenOmics app also has a fun feature where users can send a gene to a friend, such as “the hair today, gone tomorrow” gene (AR on the X chromosome), the “first” gene (HGO on chromosome 3), and the “alcohol flush” gene (ALDH2 on chromosome 12). After all, scientists have a sense of humor too.
Second only to Facebook, Twitter is a microblogging site at which users are limited to 140 characters per message. Within these 140 characters, users often include links to other online content. Anyone can read and subscribe (follow) a user’s “tweets” which are then be automatically displayed on the user’s own private Twitter screen that includes tweets from the users themselves plus the people they follow. Popular Twitter updates may also be “retweeted” which means that an interesting and meaningful message is replicated by other Twitter users to share with their own group of followers so that the retweeted message spreads virally through the Twitter community. It’s also possible for Twitter users to categorize the people they follow into groups (lists). Some users have created Twitter lists made-up of scientists or people who tweet about science, such as science writer David Bradley’s list of 499 Scientwists.
One of the more interesting uses of Twitter has been during conferences when attendees tweet live updates during events. There has been some controversy, however, about live conference coverage on social networks like Twitter and blogs. In 2009, Daniel MacArthur of the Sanger Institute live blogged the Cold Spring Harbor Biology of Genomes meeting and ran afoul of a policy that asked participants to ask conference speakers for permission before making previously unpublished results public online.
MacArthur writes, “It’s worth mentioning that scientists can benefit from having their work discussed online. A fairly hefty proportion of the readership of most science blogs consists of other scientists, so having your work disseminated in these forums both increases your profile within the scientific community, promotes thoughtful discussion of your work and can lead to opportunities for collaboration – precisely the same benefits that scientists seek in presenting at a conference in the first place.”
In an interview with Dr. Val of Better Health, American Medical News Copy Editor Pam Wood shares her secrets to great tweeting:
The first thing you have to do is read what others are writing. Some people use Twitter simply to broadcast themselves, but I think Twitter works best if you also read what others are writing and engage with them in some manner – whether it’s retweeting them or having side conversations via direct messages. Otherwise you seem like a robot.
LinkedIn is currently the most popular professional network online although other social networks have been developed that specifically target scientists. Scientists may think they do not need to use a social network to further their careers but as more information moves online, ignoring this essential aspect of career development would be a mistake. When it comes to finding a new job, recruiters and human resource managers routinely use LinkedIn to find and perform background research on potential job candidates.
The most important feature of LinkedIn is the personal profile consisting of work and education experience presented in much the same format as a curriculum vitae or resume. Like other social networks, LinkedIn users “connect” with other users who they’ve had a relationship with in the past. Any of these connections can then write online recommendations for the user that are publicly displayed in his/her profile. Being able to see the network of people to whom one is connected either directly or via one’s connections is a helpful resource as well.
Not only can scientists benefit from LinkedIn in terms of career development, they can also network further by joining LinkedIn groups. Discussions, links to news, and job postings are commonly found at LinkedIn groups where members can also consult each other on career-related concerns, such as reasonable salary requirements, interview questions, the state of the job market, and office environment.
Facebook, Twitter, and LinkedIn serve different needs. For scientists who are more interested in the personal side of social networking, Facebook is the place to be. Scientists who want to get involved and stay up-to-date quickly should try Twitter. And LinkedIn is the social network to use for personal career management and planning. Even when these sites cease to exist (as ephemeral as the Internet can be), there will be others to take their place that will enhance the way we interact with one another. For better or worse, no one can live without having an online presence and it’s important to manage what people see and hear of us on the Web.
Medical student and medical blogger Bertalan Mesko of Scienceroll.com has made extensive use of social networking. He says, “Blogging and Twitter don’t just help me in my research but totally changed the way I interact with other researchers and collaborators. Now I receive the majority of my conference invitation through my blog where I can also share and find valuable and relevant content for my research. Through Twitter, it became easier and more efficient to make new contacts with people with the same interest. We can share interesting publications, discuss recent scientific issues or get help whenever we need it. The tools of web 2.0 are seriously changing the way I experience science.”
In part 3 of the Scientists and Social Networking series, HUGO’s social media plans will be unveiled.
by Hsien-Hsien Lei, PhD, HUGO Matters Editor
TechCrunch announced the launch of Sciencefeed last week, a Twitter-like, FriendFeed-like platform for scientists to “post short microblogs (not restricted to 140 characters) on scientific headlines, new findings, controversy, conferences and ideas related to science.”
While I haven’t had the chance to try Sciencefeed, I’m not convinced that we need yet another social network when most of us already belong to fully functional networks with well-established scientific communities. I don’t know about you, but I don’t have enough time to invest in building up a profile on yet another social network unless one of my existing haunts goes kaput. Hopefully not too soon!
For scientists who are interested in trying out social networking, I’ve written a primer that will be posted here at HUGO Matters in four parts. Today, we’ll explore science blogs. On Wednesday, I’ll post more information on social networks such as Facebook, Twitter, and LinkedIn. On Thursday, HUGO’s social media plans will be unveiled. And on Friday, I’ll share some tips for scientists on blogging and social networking.
As always, please leave your questions and feedback in the comments. I look forward to hearing from you!
Scientists and Social Networking (Part 1)
Scientists and researchers are discussing, debating, and sharing information on the latest developments in science, but they aren’t doing it at Friday journal clubs held in department meeting rooms. The hottest journal clubs are now held every day of the week at all hours of night accessed from locations that are as intimate as living rooms and bedrooms and as isolated as laboratory benches. Where can you find others of like scientific mind to hash over ideas? At blogs and social networking sites, such as Facebook, Twitter, and LinkedIn.
Science blogs that focus on specific topics, such as genetics, are like social media hubs that contain a core of original content plus links that connect to other sources of relevant and interesting information. At their most basic, blogs are websites that have three main characteristics: 1) content is ordered in reverse chronology starting from the most recent, 2) each article (post) has an area where readers can make comments, and 3) posts contain links to other online content. As blogs have evolved, however, some are becoming similar to online magazines with featured posts, image galleries, forums for interactive and reader discussions, in addition to regular updates on current events.
Scientists with a flair for writing find blogs to be the most flexible way to dissect the latest research, express opinions, share personal experiences, and discuss the results of experiments among other uses. Science bloggers have also found a strong community on the Web that gives them the chance to network. Through blogging, scientists are able to get and give advice on a variety of concerns that affect their everyday life: study design, grant writing, science policy, teaching, research in academia, research in the private sector, career development, office politics, etc. On blogs, essays of any length can be posted within minutes and soon after, an exchange between writer and readers often begins, sometimes lasting days on both the original blog and between blogs. Blogs are like digital soapboxes where anyone can claim a spot on the Web for commenting on topics that strike their fancy, including science, while the audience chimes in.
Keith Robison, lead senior scientist at Infinity Pharmaceuticals and author of Omics! Omics!, says of blogging, “One of the original appeals of blogging for me was to actually write thoughts in paragraphs! Especially in the corporate world, too often we just jot bulletpoints. Not only have I been fortunate to receive thoughtful comments on the blog, but I have, in a few cases, been tipped to upcoming news. I’ve always loved news, so to be a quasi-journalist is a thrill.”
Starting a blog is quick and simple. The beginning blogger can select from a number of free blogging services* that offer storage, template designs, and blogging software. Alternatively, tech savvy bloggers can install a blog on their own server space. The mechanics of blogging are very similar to word processing but with other added features, such as images, video, audio, and widgets featuring content from other websites. Blog networks, such as ScienceBlogs.com, offer experienced science bloggers technical support and blog hosting in an ad-supported environment. Each type of blog has its pros and cons depending on a scientist’s technical abilities and what he/she is able to devote to blogging.
Tomorrow, part 2 of the Scientists and Social Networking series: Science on Social Networks.