Modelling in molecular biology: describing transcription regulatory networks at different scales

first_imgApproaches to describe gene regulation networks can be categorized by increasing detail, as network parts lists, network topology models, network control logic models or dynamic models. We discuss the current state of the art for each of these approaches. We study the relationship between different topology models, and give examples how they can be used to infer functional annotations for genes of unknown function. We introduce a new simple way of describing dynamic models called finite state linear model (FSLM). We discuss the gap between the parts list and topology models on one hand, and network logic and dynamic models, on the other hand. The first two classes of models have reached a genome-wide scale, while for the other model classes high-throughput technologies are yet to make a major impact.last_img read more

Open letter criticises London Student closure

first_imgThe letter ends by demanding that university management “reconsider the scrapping of such an important and valued institution”.The newspaper will ceased to be funded by the University of London at the end of this year, as part of the restructuring of ULU, which is having its sabbatical officer positions abolished and is transferring it services and facilities to a ‘student centre’, to be run by the University. The decision to close ULU came as a result of a review of the federal students’ union undertaken by the University last year, following concerns raised by a number of College Students’ Unions about ULU. The report concluded that ULU had largely outlived its usefulness. However, funding for London Student, which is published by ULU, was not discussed in the report.Following the decision to close ULU, University of London Union president Michael Chessum requested that university managers provide a one-off payment of £54,000 spread across the university’s 19 constituent colleges, so that the newspaper would have time to secure alternative backing.In a meeting last week, the Vice Chancellors of Colleges turned down the request for funding, with the final decision going to a meeting of the University Trustees on 16 July.The newspaper has previously published stories that have been picked up by national newspapers. In 2006, London Student published a story exposing that the Mail on Sunday had offered student reporters money to record meetings of student Islamic societies, following the 7 July 2005 London Bombings. The paper also revealed that the leaving party of UCL’s provost Malcolm Grant had cost the college more than £17,000. London Student also experienced controversy, in 2013, when its annual election for editor was rerun, following complaints that the newspaper had been bias in its coverage of the election. The controversy centred on a ‘Random Facts’ section of the newspaper’s ‘Election Special’, which described one of the candidates, Katie Lathan, who was a deputy editor of the London Student at the time, as possessing “over 20 nominations from teams and societies across the University of London”. Meanwhile, another candidate, Oscar Webb, was described as never having “been involved with London Student.” Webb was eventually elected editor unopposed in the rerun of the election, after Lathan withdrew.In a statement, President of ULU Michael Chessum, said, “The University of London is engaged in an act of vandalism against organisations and activities that have taken students decades to build up. It costs peanuts to fund London Student, and it is profoundly sad that Vice Chancellors will not put forward funding for a vital source of community, news and scrutiny – but then of course, why would they?”Oscar Webb, the current London Student Editor, said, “London Student has been a necessary and valuable asset to the University for the past 60 years. As we’ve seen recently with the examples of the Garden Halls and some of the special collections, the current management at UoL seem intent on selling-off this legacy.”Max Needham, a student at Royal Holloway, commented, “To be honest, I don’t think many ordinary students will miss it. Most of the colleges have great newspapers anyway, which are more relevant to those who read them. At Royal Holloway we have The Founder and The Orbital, which have always been far more interesting than the London Student with their focus on events more local to our community. They often cover the big University of London stories anyway.”After shutting down student politics, the Univ of London now wants to silence student voice. Save @LondonStudent! http://t.co/CrCNPAWdnP— Aditya Chakrabortty (@chakrabortty) July 15, 2014 Several prominent journalists, including The Independent‘s Editor-in-chief Amol Rajan, have signed an open letter criticising the decision of the University of London to stop funding the London Student newspaper as “an affront to free thought”.The open letter, published in The Guardian, has been signed by London Student alumni; academic staff at University of London colleges and a number of professional journalists.London Student is the student newspaper of the University of London Union (ULU), and has existed in its current form since 1979. The university has had a student-run newspaper, funded by the University, since the 1920s.The newspaper claims to be the largest in Europe, with over 12,000 editions of the newspaper printed each fortnight during term time although the Norwegian student newspaper Universitas also makes this claim and has a circulation of 17,000 copies.The letter is signed by 17 former editors of the newspaper, as well as academic staff from various constituent colleges of the University of London and Imperial College London, which became independent from the University of London in 2007.The letter was also signed by professional journalists, including Aditya Chakrabortty, Senior economics commentator at The Guardian, Alexi Duggins, Editor-at-large of Time Out, Henry Langston, Editor of Vice News UK, Laurie Penny, author and contributing editor at the New Statesman, and The Independent‘s Rajan.In the open letter, it is claimed that “there are political overtones to the university’s abrupt planned closure of the newspaper”. The letter also adds that, “London Student is one of the few student-led outlets where students can learn and exercise the critical skills they will need to challenge orthodoxy and power; shutting it down is an affront to free and radical thought on campuses, and is an insult to future generations of students.”last_img read more

Graduate students find challenges rewarding

first_img “Classes tend to be primarily discussion based rather than test based,” Smith said. “They involve reading a lot of primary literature that is being published in science journals.” “A stipend is essentially a paid salary for your work as a graduate student,” Smith said. “With a research assistantship, your advisor is responsible for paying your salary through his research funding.” Though students traditionally go straight from undergraduate education to graduate school, Tang took a detour. She had a part-time job where she assisted a professor investigating potential environmental and genetic factors involved in autism. After graduation, she was offered a full-time position in the professor’s lab, which guided her toward her current position.  “As an undergraduate, you should go beyond the simple class requirements and seek out opportunities to get experience. Not only does this increase your chances of getting either a good job position or admittance to a professional degree program,” he said, “but it allows you to experience a field of work so that you can decide now, rather than later, if it is something you would like to do.” “I was lucky to have been introduced to a field that I am so intrigued by,” Tang said. “When inquiring into undergraduate research opportunities, I was not able to join the original lab group that interested me. I ended up in one that shaped my career as a research scientist,” he said.  Graduate students with paid stipends, Smith said, are not permitted to have any other jobs. Tang found that with her demanding course and research workload, there would be no time for an outside job, even if allowed one. “Graduate school is a full-time position,” Tang said. For Tang, life off campus allows for separation between her work and personal life. Frederick said that preparation is key, especially as an undergraduate. “The biggest piece of advice I have for undergraduates is to not be afraid to speak to your professors, TAs or professionals in the field that you are interested in. Ask questions about what they thought of their program of study, if there are any faculty members accepting students for the upcoming year and even what they believe would be the best fit for you,” Tang said. “People love to share their experiences with future graduate students.” Frederick’s course load requires him to take three core classes and three other electives, one of which must be in his field of specialty.  Frederick said this ultimately sparked his interest in protein dynamics using Nuclear Magnetic Resonance.  “So much of my time is spent working in the lab, which is off campus, or in classes,” she said. “I appreciate [having] the time at home to unwind.” Teaching assistant by day, researcher by night — add on another 30 to 50 hours of reading and studying, take into consideration some driving time, and you begin to have a clearer image of the life of a graduate student at Notre Dame.  Graduate students also take advanced classes on their topic of interest, Smith said. Students in the Ph.D. program have to take two classes a semester for the first two years of the program, and then one credit worth of classes afterwards.  Victoria Smith, a graduate student in her second year of a Ph.D. program in the biology department, assists in a freshman biology class.  Through a teaching assistant (TA) position, graduate students can receive a stipend for their services, she said. Graduate students also obtain stipends through fellowships they have been awarded, or through a research assistantship. Though there is the drawback of commuting to work every morning, an especially difficult task on football weekends, Smith is able to have pets and plant a garden. These graduate students said living off campus has its benefits.  Smith estimates approximately 45 to 55 hours of her week are devoted to research in the lab, in addition to her work as a TA and reading at home.  After graduate school, Smith said she will likely stay in academia as an assistant professor at a university. Tang hopes to continue working with children with autism and their families.  Thomas Frederick, a first-year chemistry and biochemistry graduate student, entered his field of study by accident. For undergraduates looking to go to graduate school, Tang suggested thinking about it early.  “The stipend that I receive from the University of Notre Dame allows me to devote my time to research and academics, without having to worry about taking an outside job to pay for daily living expenses,” Tang said. “It is an honor and a privilege to have the opportunity to just learn and think.” Karen Tang, a first-year clinical psychology doctoral student, works in a less visible position, focusing her energy into research. Tang spends the majority of her non-class time in the lab, reading articles in her area of interest, attending meetings and working with undergraduate research assistants.last_img read more