Understanding how complex phenotypes arise from individual molecules and their interactions is a primary challenge in biology that computational approaches are poised to tackle. We report a whole-cell computational model of the life cycle of the human pathogen Mycoplasma genitalium that includes all of its molecular components and their interactions. An integrative approach to modeling that combines diverse mathematics enabled the simultaneous inclusion of fundamentally different cellular processes and experimental measurements. Our whole-cell model accounts for all annotated gene functions and was validated against a broad range of data. The model provides insights into many previously unobserved cellular behaviors, including in vivo rates of protein-DNA association and an inverse relationship between the durations of DNA replication initiation and replication. In addition, experimental analysis directed by model predictions identified previously undetected kinetic parameters and biological functions. We conclude that comprehensive whole-cell models can be used to facilitate biological discovery.
The Orb is a data visualization showcasing research projects associated with the Institute for Creativity, Arts, and Technology (ICAT) at Virginia Tech. I began working on this project with the intent of just creating a few graphics that one of our undergraduate design student might use in some promotional materials. A little bit of code here…a little bit go code there…and the next thing I knew, I had a full blown visualization on my hands. While this version has a lot of core functionality, I am still thinking about next steps for extending this to a larger data set and expanded interface.
I take a lot of pride in having done this in Processing. As an artist that only started learning code a few years ago, I am still fascinated by the idea of writing words to create graphics.
Props to my collaborator Noha ElSherbiny (PhD student in Computer Science at VT). She handles all of the data analysis, generating the values that drive the connections.
Visualization: Dane Webster (me)
Data Mining: Noha ElSherbiny
Additional Concept Designs: Audrey Pfund
Music: Chris Zabriskie (chriszabriskie.com)
Ask anyone who works in international development about the challenges that come with improving peoples’ lives half-way across the globe and you’ll probably get an earful about funding, difficult collaborations, weak infrastructure, etc. The list could go on! In my opinion, however, there is no challenge in international development greater than the gender challenge.
Almost all international development aid must integrate a gender component into the work to ensure that aid investments and benefits are equally distributed between men and women. According to USAID’s Policy on Gender Equality and Female Empowerment, integrating gender “involves identifying and addressing gender inequalities during strategy and project design, implementation, and monitoring and evaluation. Since the roles and power relations between men and women affect how an activity is implemented, it is essential that project managers address these issues on an ongoing basis.”
After researching gender in international development for a couple of years now, I can assure you this is easier said than done.
To better understand the challenges of gender research in international development, I asked my supervisor, Dr. Maria Elisa Christie, director of the Women and Gender in International Development at OIRED, what she thinks are the biggest obstacles regarding gender work and how we can overcome them.
“Women don’t get involved in our projects as often as men. . . and there are many reasons why,” explains Christie. Among researchers, “there is sometimes a mentality where they ‘want to speak with farmers,’ but don’t realize that women are farmers also, even if the household only identifies the husband as the farmer.” This perception can be particularly constraining when it comes to including women in trainings and successfully implementing interventions. “When there is a meeting or training, usually only one person is invited for each household,—and this is usually the husband or male farmer.”
Regarding gender equity in research teams, the struggle to include women is not necessarily participation, but rather experience and education. “While we encourage our research teams to have an equal number of men and women,” says Christie, “the fact is, in the US as well as in the countries where we work, there are fewer women in many of the sciences that we work in, such as soil science and entomology.”
So how do we overcome these barriers? “Well for one, invite the women,” says Christie. “Women are usually interested and will come if they are invited. There are obstacles though, even if they are invited. Sometimes men don’t want them to come, and the women usually have so many household chores that they feel they can’t come.” But researchers can consider factors that will increase the likelihood of women’s participation. These include picking a venue that is not far from women’s homes, and conduct trainings of short duration over a longer period of time (such as two-hour trainings once a week for a month) versus trainings of long duration over a short time period (such as four-hour trainings every day for one week).
“One of the things that gender researchers have known for years, which is rather simple,” Christie says, “is picking a time and place that make workshops and trainings accessible to women, which might differ from men.” Researchers also need to be aware that some women will not participate in mixed groups, a custom Christie ran into during her research in Bangladesh and Indonesia.
“When men and women don’t meet together, it is especially important to have female trainers and hold events for women in addition to those for men. Luckily, we had women scientists in those two countries to help with the women’s training.”
It is also important to have a topic that is a priority for women. “If we’re talking about a crop that is under men’s control, women may be less likely to have any interest. We need to listen to women’s voices and see what they want.” Christie explains one way to get their input is to work directly with women’s organizations. These groups provide women the opportunity to gain skills, confidence, and leadership positions.
Christie also stresses that researchers should use participatory methods such as focus groups and interactive exercises to encourage farmer participation. By using these methods, “we can learn about men’s and women’s knowledge, which goes beyond a general understanding of farmers’ crops, pests, and soils. These methods can further our understanding of whether interventions are appropriate for a certain area, and for whom they are appropriate.”
To keep us humble and our egos appropriately-sized, Christie has one final recommendation. “There are gender experts, both men and women around the world who are proficient in addressing gender issues and reaching women. It is important for us to not to come in with our own agenda, but to work with local women’s associations and gender experts in our collaborating institutions who know the issues, the culture, and the interests of women in the places we are working.”
Easy, right? Even though Christie’s strategies seem relatively simple, there is more to them than meets the eye. If everyone took these recommendations into account, many more people would be educated and fed. Maybe one day these challenges will be in the past, but until then, Christie has her work cut out for her!
The capsizing of a passenger ferry in South Sudan on Jan. 12 is a tragedy enfolded within a tragedy. Two hundred people died trying to escape the recent eruption of violence that is tearing South Sudan apart. Anyone younger than 30 years old on that ferry had experienced no more than eight years of peace during their lives. The BBC and other news outlets explained the bare facts of the sinking, associating it with a sudden displacement of 350,000 people fleeing the fighting or in fear of it.
It is hard to get our mind around the magnitude of numbers that are daily presented to us in the news, especially numbers relating horrific events. Reading about the ferry, I remembered an article in the Washington Post many years ago that overlaid the density of landmines in Sarajevo during the war in Bosnia Herzegovina onto a map of the Washington Mall. Readers could sense the danger they would face traversing a familiar landscape. Thinking about 350,000 people fleeing from their homes in South Sudan, I wondered how it could be portrayed in a way that would help me grasp its magnitude using the Virginia geography with which I am familiar.
Following the I-81 corridor from the Tennessee border, it takes the population of seven counties to reach that number. The internal displacement of people over the past month in South Sudan is as if every person in the seven counties along 170 miles of I-81 suddenly left.
How else might visual similes make news easier to comprehend? Since 2011, 100,000 people have died due to the war in Syria. If every life lost in Syria were represented by a candle, could you stare at a light source held in your hands without going blind? (No, according to my rough calculation.) If it didn’t blind you, would it be a less effective simile?
I am not an “app” person. My phone’s intelligence is far below average. Nevertheless, I wonder. Would it be handy to be able to present numbers from the news and portray them in a personal and customizable way that takes advantage of landscapes and imagery familiar to each reader? Online news sources continue to provide new ways to interact with their content. What if there were a standard format that news providers could use to link data embedded in their articles to an app that would help you understand in a more personal way the numbers and statistics in the news? I do not develop apps, so all I did was come up with two possible names. First was “In My Backyard” (in contrast to “not in my backyard”). That is not mellifluous like Twitter, Flickr, or Instagram. “Similese” later came to mind.
There is already a great amount of professional graphic and cartographic creativity embedded in our news, much of it incapable of being modeled at familiar scales. For example, recently, the Washington Post featured forty maps that help us better perceive our world. Map number 37 happens to use the “What if it were my backyard?” approach. While you are in the neighborhood, make sure to look at video map number 40. It is mesmerizing.
Coming back to South Sudan, let’s not forget the ability of traditional photography to convey a story effectively. Check this out: “This depressing image sums up why things are so bad in South Sudan,” by Max Fisher. You may note the estimate of displaced persons in his article is 200,000 people.
This post comes to us with input from Sandra Black, working on communications for the Education and Research in Agriculture in Senegal program.
A service-learning trip to Senegal was organized during Virginia Tech’s new winter session to provide an immersion learning experience for Virginia Tech students. The group of 13 began their two-week trip in the capital, Dakar, and travelled along the coast of Senegal, from Saint Louis in the north down to Toubacouta, near Gambia.
The group was led by three Tech professors: Cindy Wood—professor of animal and poultry sciences; Ozzie Abaye—professor of crop and soil science; and Matthew Eick, also professor of crop and soil science. The course is called Service-Learning in the Developing World: A First-Year Experience. While the course is designed for freshmen, not all of the participants were first year students. The students did everything from tree planting with Senegalese students to collecting grasses with villagers for silage production to helping out on a water purification project. Wood talks about the design of this course in an article about winter session here.
Photos can be found on our Flickr page, but here’s a sampling of the students in action:
The Launch Place is bringing businesses to Southern Virginia. As the leading entity to recruit and support entrepreneurs in the Dan River Region, the organization announced its first seed fund investment in KSI Data Sciences.
KSI will receive an initial investment of $150,000, and another $100,000 after successfully testing its prototype for video and data management solutions used in remote sensing platforms on unmanned aircrafts, vehicles and mobile devices. The KSI team plans to relocate to the Dan River District later this month.
Formerly called the Southside Business Technology Center, the Launch Place has assisted start-ups and early stage companies since 2005. After receiving a $10 million grant from the Danville Region Foundation in 2012, the organization was able to add seed funding to its capabilities as a business incubator and rebranded itself as the Launch Place.
What makes the Launch Place unique is its strategy of recruiting entrepreneurs, and then providing the support to allow their businesses to organically grow in the Dan River Region. Through a partnership with VT KnowledgeWorks, entrepreneurs in the program receive free mentoring through the planning, launch and growth stages of starting a business. The Launch Place team also provides a variety of business consulting services, including business plan development, market research, financial modeling and competitor analysis.
The Launch Place helps entrepreneurs reduce start-up costs by offering residential housing and office space subsidies to entrepreneurs that commit to stay in Danville for three years. The Dan River District provides a great place to live, work and play through its historic downtown area, riverfront walking and biking trails, plentiful water sports, concerts, festivals and other recreational activities.
A view of the Launch Place headquarters in the historic downtown area of the Dan River District.
At 1:07 p.m. today, Orbital Sciences successfully launched its first resupply mission to the International Space Station from Pad-OA of the Mid-Atlantic Regional Spaceport at NASA’s Wallops Flight Facility on Virginia’s Eastern Shore.
Orbital Sciences’ Antares rocket launched the Cygnus spacecraft into Earth’s orbit, where it is currently traveling towards the ISS at approximately 17,500 mph. The spacecraft is expected to rendezvous with the ISS early Sunday morning.
Cygnus is carrying 2,780 pounds of supplies to the Expedition 38 crew, including science experiments, provisions for the crew, spare parts and experiment hardware. The payload includes 23 science experiments that will involve more than 8,600 students across the U.S. and Canada.
Known as the Orb-1 Mission, this is the first actual resupply mission to the ISS following a successful demonstration mission to the ISS in September.
As part of its $1.9 billion Commercial Resupply Services contract with NASA, the Orb-1 Mission is the first of eight resupply missions to the ISS, expected to deliver approximately 20,000 kilograms of cargo through 2016.
The Orb-1 Mission comes right on the heels of a positive announcement from the Obama Administration — the president approved an extension of the ISS through 2024, allowing for the possibility of more resupply missions past 2016.
The success of today’s launch is another illustration of Virginia’s leadership in the space industry. Through MARS, Virginia offers one of only four commercial sites authorized for orbital space launches.
To learn more about Virginia’s thriving aerospace industry, click here.
A view of the Antares rocket ready for launch from Pad-OA of MARS at NASA’s Wallops Flight Facility in Virginia. Photo courtesy of NASA/Bill Ingalls.
As member of the editorial board of Trends in Biotechnology, I thought it might be useful to identify the Trends in Biotechnology articles that generate the most “buzz”. Below are the articles that have been mentioned in social media at any time. Click on any of them to know more. Sort the table by number of FaceBook postings, Tweets, and Blogs talking about these publications. You can also click on the the Analytics column to sort the publications according to their Altmetric score.