Travel grant reports 2014
Lyuba Zehl, Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6), Jülich Research Centre and JARA, Germany
Purpose: Participation in the AREADNE conference 2014, Nomikos Conference Centre, Santorini, Greece
I would like to thank the INCF for awarding me with a travel grant to the conference "AREADNE 2014" (conference for Research in Encoding And Decoding of Neural Ensembles, Nomikos Conference Centre, Santorini, Greece). There I had the chance to give a poster presentation on my work “Metadata management for complex neurophysiological experiments” and to discuss my main PhD project on advanced analysis of massively parallel multi-electrode recordings with prominent members of the neuroscientific community. The four-day program of the AREADNE conference consisted of 22 neuroscientific talks (speakers: G. Laurent, T. Mrsic-Flogel, A. Tolias, C. Petersen, W. Gerstner, S. Tonegawa, O. Paulsen, L. Frank, J. Raymond, K. Britten, G. Kreiman, B. Wandell, EJ Chichilinsky, T. Sharpee, J. Pezaris, E. Marder, D. Margoliash, M. Churchland, T. Sanger, S. Ganguli, S. Grün, P. Sabes), three poster sessions, and many possibilities to socialize, discuss and exchange experience with all participants of this meeting.
During my poster presentation, but also during several discussion time slots of the meeting, I tried to raise awareness for the known, but often not systematically addressed problem of reproducibility of neurophysiological experiments and analysis. Based on an example from our collaboration with the experimental laboratory of A. Riehle, I explained the usefulness of a standardized and well-organized metadata collection using odML (open metadata Markup Language, developed by J. Grewe, T. Wachtler and J. Benda 2011) to handle data and their analysis of a complex behavioural (reach to grasp) experiment that yields massively parallel spike and LFP recordings. Especially those scientists I spoke to who also face a large amount of data recorded in rather complicated experiments (e.g., C. Petersen, R. Goebel, N. Hatsopoulos, C. Anastassiou, S. Kandler) were well aware of the importance of well-organized metadata management and highly interested in how we dealt with this issue. As a feedback, I learned that besides the Python-based odML library we are using, the demand for a MATLAB library with similar features is high. I also learned that the effort we currently spend to better document the Python-based code and to provide a detailed user tutorial which includes use cases on how metadata can be structured and how metadata collections can be integrated in a general workflow (from experiment to analysis) is highly appreciated by the community.
Besides the successful poster presentation, I was able to discuss my main PhD project on the analysis and interpretation of oscillatory features of massively parallel local field potential recordings from motor cortex during a delayed reach-to-grasp task (Riehle et al. 2013, Front Neural Circuits 7:48) with some neuroscientists working on similar or related topics, or using similar recording equipment (e.g. N. Hatsopoulos, M. Vaidya, M. Best, R. Shewcraft, P. Sabes, A. Riehle, F. Sinz, J. Cotton). I received some valuable feedback on my current results, problems and ideas which will help me to improve my work in my PhD project.
The purpose of this travel grant was to allow me to visit the laboratory of Theoretical Neurobiology lead by Prof. Michele Giugliano at the University of Antwerp. Here, I have designed, implemented, and refined a data analysis tool chain, along the lines of the work recently published by Giugliano (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3958706). However the previous approach was developed for data coming from dissociated neuronal cultures, while my adaptation enabled me to apply the same tool set to analyse the electrical signals recorded from acute rat brain cortical slices, recorded with 3D Arrays of substrate-integrated MicroElectrodes (MEAs), upon pharmacological and ionic manipulation of the extracellular medium.
During my stay in Antwerp, I have consolidated previous theoretical concepts I had been previously exposed and for the first time I could apply them to real data. I have also learned new methodologies, which have been directly inspired from biophysical mathematical modelling studies. Specifically, by focusing on layer V microcircuits of the primary somatosensory cortex and applying MATLAB analysis script that I contributed to refine and adapt to my experiments, I have found a direction for uncovering fundamental features of neuronal network dynamics that would not otherwise be captured. As I plan to pursue this research beyond my master project, during a future possible PhD career trajectory, such a direction has been extremely precious and important for shaping and guiding the next step.
Thanks to this INCF-sponsored visit, I have overall expanded my experience in computational modelling and learned new data-analysis methodologies and tools to deal with a variety of features of multichannel spike train analaysis. This visit represented my first research experience abroad, and as such it has been essential to reveal my potential. I am convinced, it will influence the future direction both of my career and of my research interest.
Finally, thanks to INCF, I had the opportunity to attend the 2014 NERF Neurotechnology Symposium “Biological & Engineered Neural Circuits” held in Leuven (Belgium), during the same period of my stay.
Host: Espen Hagen, IMT, Norwegian University of Life Science (NMBU), Ås, Norway
- Collaboration: The one week of full-time collaboration focused on this project brought EH and me a step forward. We were able to discuss previous work and to set our next goals and we made progress in the implementation of both our network model and model-specic analysis and visualization tools. We had fruitful discussions with Hans Ekkehard Plesser, one longtime developers of NEST and the Topology module, on our model assumptions when topological connections are incorporated, in particular handling of connections toward the boundaries. Furthermore, I was introduced to the group and to the group leader Gaute T. Einevoll, with whom we discussed the project details and also the premise of incorporating biophysically detailed model activity measurements such as LFPs and VSD signals.
- Model development: During the lab visit, the network model was extended by several features, e.g. connection proles with dierent distance-dependent distributions for connection probabilities have been implemented in such a way that the whole number of connections is preserved. In addition, a method to account for missing lateral connections in networks without periodic boundary conditions was considered.
- Analysis tools: The base area-specic analysis and visualization routines were functional after this week. We chose a modular structure (Python classes) that allows for integral utilization of available and inhouse developed Python resources such as Sumatra, NeuroTools, Neo, Neurotools, and ElePhAnT.
Viktor Tóth, Department of Measurement and IS, BUTE, Budapest, Hungary
Purpose: NCBS CAMP Computational Approaches to Memory and Plasticity, Bangalore and research visit to Upinder S. Bhalla’s lab
I stayed in India for 6 weeks of which I spent 2 weeks attending the course of Computational Approaches to Memory and Plasticity and establishing a joint project of fear conditioning and extinction. I had a week for sightseeing around South-India, and for 3 more weeks I worked in collaboration with Upinder S. Bhalla’s lab optimizing the MOOSE software by re-implementing parts of the Hines solver, solving the profiling of the code and providing the possibility to do parameter searching using MOOSE models.
My contributions to MOOSE are not by any means done; I still have to work on the Hines solver implementation and there are also some solvers left to optimize by GPGPU.This trip to India shaped my perceptions of my future studies very much; now I have an ambition to get involved in computational neuroscience, and search for universities and funds around the world to make it happen. All in all, it was a wonderful experience getting to know so much kind and utmost intelligent personality, not to mention knowledge I gained from the lectures of the CAMP course. I mean, I don't remember if I had any this sort of
intensely great time before in my life. More detailed information about the fear conditioning project and my contributions to MOOSE can be read on my blog at http://neuroinf.blogspot.com
Bernhard Kaplan, Department of Computational Biology, KTH Royal Institute of Technology, Stockholm, Sweden
Purpose: International Summer School on Complex Networks in Bertinoro, Italy, July 14-18 2014
The summer school included 33 hours of lectures with the possibility to discuss with the speakers during and after the lectures. The courses provided a comprehensive overview of the methodology of applying complex networks to various fields giving by international renowned leaders of the field (list of speakers include: Michele Benzi, Luciano Costa, Ernesto Estrada, Jesus Gomez Gardenes, Edwin Hancock, Ferenc Jordan, Yamir Moreno, Mirco Musolesi, Simone Severini, Richard Wilson). First, the focus was put on general concepts and the algebraic formalism of describing static (i.e. temporally not changing), undirected graphs. This includes the classification and characterization of different network types and the different ways of how to assess the importance of nodes in the graph. Second, we learned about temporal networks, i.e. networks in which the interactions among a set of elementary units change over time, which are particularly relevant in the context of plasticity in neuroscience. Third, the learned concepts were applied to various examples, like the spread of diseases, ecological and landscape networks (food webs), social networks, game theory and the evolution of strategies using different types of graphs. Of particular importance for neuroscience is the approach of multi-level modelling used e.g. in ecological networks by coupling different levels of description. Finally, we dealt with advanced topics and unresolved problems in complex networks which is generally speaking the question how to efficiently compare and generate different classes of complex networks.
Outcomes: After attending the summer school I have the feeling of having a broad overview over the activity and unresolved problems in the field of complex networks. Furthermore, I see the opportunity in combining my field of work with the methods learned during the school and hope to pursue this direction in the near future.
I would like to thank INCF for supporting my attendance at this very exciting and informative summer school.
Jacqueline A. Fairley, Emory University, Atlanta, Georgia, USA
Purpose: knowledge transfer from Emory University (Atlanta, Georgia, USA) to the Laboratory of Knowledge and Intelligent Computing (Arta, Greece)
The primary agenda of this INCF travel grant involved implementation of a knowledge transfer from Emory University (Atlanta, Georgia, USA) to the Laboratory of Knowledge and Intelligent Computing (KIC) supervised by Dr. Chrysostomos Stylios at the Technological Education Institute (TEI) of Epirus (Arta, Greece). During my visit to TEI, I focused on the completion of two specific aims. Specific Aim 1 consisted of establishing a collaborative human sleep research triad between Emory University, KIC, and the General Hospital of Arta. Specific Aim 2 involved the development of a working plan between the KIC computational team (postdoctoral fellows Petros Karvelis, Ph.D. and George Georgoulas, Ph.D.) and the Emory University sleep medicine group (Jacqueline A. Fairley, Ph.D., Donald L. Bliwise Ph.D., and David B. Rye, M.D., Ph.D.) to develop computerized clinical decision support systems to process human overnight polysomnograms (PSGs)/sleep records collected from the General Hospital of Arta for automatic diagnosis of obstructive sleep apnea, rheumatic, cardiovascular, muscular and neuromuscular diseases. In order to complete Specific Aim 1, Dr. Stylios, Drs. Karvelis and Georgoulas, and I met with the Directors of the Sleep Clinic and Intensive Care Unit at the General Hospital of Arta (GHA), Styliani Bastini M.D. and Nathaniel Christodoulos M.D., respectively. During this meeting a working plan was established regarding the data transfer of de-identified human PSGs from the GHA to the KIC laboratory. In this discussion I provided Dr. Bastini with suggested data acquisition settings such that we obtained optimal PSG exportation, compatible with our current MATLAB® based bio-signal processing scheme. Further information regarding this collaborative effort is documented in the following press release: http://www.monoplio.gr/index.php/xamperia/2082-synergasia-tou-genikoy-nosokomeiou-artasme-to-emory-university-hospital-tis-atlanta-ton-ipa-kai-to-tei-ipeirou
Specific Aim 2 required the development of a working plan between the three aforementioned academic (TEI and Emory University) and healthcare (GHA) organizations. The working plan required collection of PSGs by Dr. Bastini and processing of PSGs using signal processing and machine learning techniques formulated and validated by TEI and Emory University. More specifically, my previous experience in applying signal processing techniques to PSGs collected at Emory University were translated for execution on the GHA PSG database. Also, Drs. Karvelis, Georgoulas and I confirmed the inclusion of 200 separate overnight PSGs to conduct preliminary processing for obstructive sleep apnea analysis. Gratefully this INCF-sponsored visit, marked my first experience in participating in the development of an international research collaboration. This training endeavor has vastly expanded my professional network abroad and provided me with the priceless experience of working on an international research team. I relish this opportunity in that it has positively influenced the future direction both of my career and computational research interests. Lastly, special thanks to the INCF Travel Grant Initiative for sponsoring this knowledge transfer
Purpose: To visit and collaborate with Prof. Tomoki Fukai in Riken BSI, and work on a project “Probing the interaction among correlated/oscillated inputs, spike timing and synaptic efficacy” as part of my PhD thesis
The main aim to visit the RIKEN was to collaborate with Prof Fukai and work on one part of my Phd thesis, based on his expertise. We worked theoretically on some causal plasticity rule (STDP) in – one layer – feed forward pre-post connection. Since oscillation activity has attracted a lot of attention, especially in hippocampal neurons, we tried to trace theoretically the interaction of spike timing and oscillation in a one layer feed forward network in the presence of STDP. We had some sessions there and discussed about the way we want to tackle the problem and its applications in the neuroscience. In fact some basic progress has achieved during my stay there and we are going to continue our work to finish this project.
I also finished my first study on the effect of spike timing and correlation and had fruitful discussions with researchers in Riken. I gave a lecture in Prof Fukai’s lab about my previous work and received constructive comments. Besides, I have been able to present a poster in Japan Neuroscience community (Neuro2014) and enjoyed my time there, discussing with people about correlation, spike timing, STDP, as well as visiting their posters and hearing their lectures. It is nice that I have been able to visit some other experimental labs in Riken and other universities in Tokyo, which gave me some feeling how to relate the theoretical work ahead of us to existing experiments. Altogether, I really enjoyed and learned from two month stay in Riken and I think it boosted my knowledge one step forward.
In summary, I familiarized with the RIKEN neuroscience community, unique scientific environment and insights of senior researchers in the neuroscience. Thanks to INCF travel support which made my visit possible, and gave me this opportunity to improve my understanding of theoretical neuroscience and learn from senior scientists there how to define and tackle problems in neuroscience, using statistical and physical techniques. These methods help to ask basic precise questions in neuroscience and push the field forward step by step.
Acknowledgment: I would like to express my gratitude to the INCF and RIKEN Brian Science Institute for supporting my visit.
Purpose: Route 28 Summit in Neurobiology, Fraueninsel Germany, 6th-11th Sept 2014
In the month of September, 2014, I attended the prestigious Route 28 summit in Neuorbiology, held once every two years. This years focus was Adult Neurogenesis. We were a group of 45 international students, from graduate and post-doctoral backgrounds, working in the field of Neuroscience. With diverse backgrounds of molecular biology, imaging, electrophysiology, computational neuroscience and clinical expertise, we made a multi-disciplinary congregation with some of the leading experts and neuroscientists in the field. The workshop consisted of exhaustive sessions, one and half hour long, on different topics such as Hippocampal neurogenesis in adults,
its regulation and implications in learning an memory, Sub-ventricular zone mediated neurogenesis and its role in therapy for disorders such as Stroke, neurogenesis during growth and its preservation along the time-line of development and other similar topics. Scientists such as Kai Simons, Gerd Kempermann, Georg Kuhn, Fredrico Calegari, Weiland Huttner, Amelia Eisch, Sebastian Jessberger, Nora Abrous, Alejandro Schinder, Chichung Lie, Caghan Kizil, Paul Lucasse, and Kaylene Young presided over the sessions. The emphasis was on understanding the role of neurogenesis in adults, in normal health, the enhancement which occurred as result of
enriched conditions such as exercise, learning, or by the induction of growth-factors and the subsequent decline during disease. Different models were employed ranging from in-vitro work, to rodent studies, primate experiments, and human clinical data. Techniques such as molecular biology tools, electrophysiology, imaging, and knock-in and out studies using transgenic animals and were elaborated upon. Some exciting studies such as the effect of space radiation on brain functioning in astronauts and people planning on long-term space travel,the alteration in the levels of ongoing neurogenesis in their brain and the implication on learning and memory were also discussed. Alongside the lectures, we were given the challenge of designing a research proposal within 3 days of the meeting. We were put into groups of 5, from different research back grounds. Mostly people were given topics outside their research focus so that they could read and learn more about a new aspect of the field. From coming up with an innovative question, a completely novel concept which hadn’t been worked on before, to proposing a set of experiments and suggesting methodologies, we had to complete the task and finally give a formal presentation on the last day. The topics included (1) regulation of Hippocampal neurogenesis and its specificity which gave it uniqueness over other neurogenic zones,(2) The functional implication of this specificity and (3) Role of Adult Neurogenesis in disease. Besides this we had a session called “Life Kinetics- Enrichment Experience” which was conducted by an expert in the field of physical and mental exercises which help build up cognitive ability, memory and agility. This inspired us to read and discuss much beyond our usual interest focus and come up with innovative solutions. I along with my group, which was assigned the first topic, proposed studying the branching of the “broccoli” progenitor cells in the hippocampus which extend from the Dentate Gyrus, up though molecular layer into the CA3 region. This branching is maintained through development into adulthood and seems to serve some exciting purposes of interacting with the overlying blood vessels, and the axons of other neurons and gill cells in the molecular layer. We suggested anatomical studies, along with 3 photon imaging and electrophysiology in transgenic mice to elucidate the role of these unique cells. And to our delight we won the first prize which came with a lot of appreciating for our interdisciplinary approach and incisive study plan. This summer school was a great platform to interact with scientists and students from the field. The discussion were extremely friendly and open and allowed for clarification of all doubts and queries. I would like to profusely thank the organizers of the Route 28 summit for putting up such a good meeting and bringing together such a bright group of people for sharing ideas in the growing field of Adult Neurogenesis. I would also like to extend my sincere gratitude to the INCF committee for helping me with my expenditure in terms of the registration fee which enabled me to to attend this fantastic meeting. Coming from India, which is a developing country, it is extremely difficult to get sufficient funding to attend such meetings. The INCF travel grant helps ease this and provides an excellent opportunity for young researchers such as me to interact with the international community to gain experience and understating of the fast-growing field of Neuroscience.
Purpose: NCBS CAMP Computational Approaches to Memory and Plasticity, Bangalore. 28 June - 12 July 2014
The summer school (CAMP) at NCBS, Bangalore was a 15-day summer school on the theory and simulation of learning, memory and plasticity in the brain. Given the important role that computational neuroscience methods play in my PhD thesis project, as it requires the ability to analyze data and make theoretical predictions, the CAMP school had special significance for me. During the school we had two 1 hour 30 min lectures in the mornings, hands-on tutorials in the afternoon/evenings, and also research lectures, discussions and some sessions for project work in the evenings. In special, remedial tutorials on neuroscience, math and programming were very useful to then work upwards from sub-cellular electrical and chemical signaling in neurons, onward to micro-circuits and networks, all with an emphasis on learning, memory and plasticity.Experiences and outcomes. One of the most important experiences I had during the school was in the last week when we worked on a short project to be presented the last day. With the guidance of faculty, teaching assistants and other students, I was able to use a previous computational neuronal model to gain insights into the neuronal basis for cold temperature responses in Locus Coeruleus neurons from Bullfrog. I developed a preliminary model that reproduces the behavior we observe in electrophysiological experiments. The results of this work constitute a good basis for initial studies on developmental plasticity of chemosensitivity in this specific area of the brain. The CAMP school also gave me useful opportunity to network. I established connections with Eve Marder from Brandeis University and with Michael Hauser from University College of London. I was able to visit the Indian Institute of Technology in Bangalore and expend time with students at the end of the conference. I also extended my visit after the course to initiate a study on anxiety and developmental disorders within the context of respiratory control with Dr. Sumantra Chattarji, who opened the door for an internship at NBCS and start a short research period the next year. In summary, the school helped me to gain familiarity with programming in python, with dynamical systems, and many other emerging computational neuroscience methods relevant to memory and plasticity. It also gave me the opportunity to meet professors, PhD students and post-docs from theoretical and experimental backgrounds and enjoy the academic and cultural exchange with them.
Purpose: NCBS CAMP Computational Approaches to Memory and Plasticity, Bangalore. 28 June - 12 July 2014
The aim of the visit to the NCBS - Bangalore, was the attendance to CAMP summer school (Computational Approaches to Memory and Plasticity) during July 2014, that focused of different aspects of memory, learning and plasticity from sub-cellular signaling within synapses to networks of neurons. For this summer school, the program started with tutorials on neuroscience/programming and dynamical systems, that accompanied research lectures, research tutorials from the lecturers and discussions. The school ended with the development of a short project that had to be presented at the school. Thanks to the support of the INCF-Travel Grant, I've managed to expand my expertise in computational modelling, in particular within the field of mathematical descriptions of single neuron (from a dynamical systems perspective), as well as computational tools and software for the modelling of synapses, neurons and networks. However, during this school I learned much more than those intended goals. The research tutorials from the lecturers introduced powerful tools to keep track and define research questions in general. The tutorials and discussions were great opportunities to speak to faculty and fellow students who come from strong backgrounds. The project was an exciting and challenging adventure, which was not only a great chance to learn a bit deeper about a particular idea, but also showed me how to scale projects to particular time frames...asking the right questions. This course is a great opprtunity to get familiar with advanced concepts in computational neurosciences, I would like to thank the organizers at NCBS for putting together such an intense and challenging summer school, and the INCF for making my attendance possible.
Purpose: NCBS CAMP Computational Approaches to Memory and Plasticity, Bangalore. 28 June - 12 July 2014
My aim was to familiarize myself and gethands-on experience with current research topics in memory and learning. Specifically, my goal was to build on my knowledge of single-cell dynamics to the use of network models in memory research. Lectures spanned multiple levels of modeling, from biochemical memory models to models of working memory and decision making. The summer school also provided plenty of opportunities for interactions with both students and faculty, all coming from diverse backgrounds. These opportunities were very noticeable during the intense work on student projects in the last portion of the school.
The summer school consisted of lectures, tutorials, research talks and discussions. It was structured so that research topics introduced by speakers were followed promptly by tutorials. During the tutorials students had to take active participation and implement ideas from the lecture and perform simulations using a variety of software packages, such as MOOSE and Brian. The code provided serves as a solid basis to following up with concrete implementation of any of the many ideas presented. Research talks elaborated on the topic introduced by the speaker and presented his or her current research. A central component of the summer school was the development of student projects. Projects were either self-proposed or followed up on one of the topics introduced by the lecturers who, along with the TAs, helped guide the students in their work.
The question I address in my project was the extent to which a proctolin-activated inward current affects the network activity of pyloric networks that produce rhythms with similar characteristics but that have widely differing individual conductances and synaptic strengths. During the course of my project I gained insight into the workings of MOOSE and learned how to address interesting research questions using the neuronal and network databases constructed by Prinz et al. 2003 and Prinz et al. 2004. My results suggest that the burst period of the pyloric rhythm might be pre-served under modulation but further exploration of other relevant activity characteristics is needed.
I would like to thank the organizers at NCBS for the wonderful CAMP summer school and INCF for providing me with the opportunity to attend the course.
On the first half of July 2014 I attended CAMP summer school in Bangalore in India, thanks to support from INCF. The main topic of the summer school was computational approaches to memory and plasticity. This was perfect for me, because I am seriously thinking about changing my field of study from computer science to computational neuroscience and memory models. The summer school schedule was very busy, containing number of lectures, tutorials and group activities. Every day began at 9am and finished around 10pm11pm with a 2 longer breaks for lunch and dinner and 2 short ones for coffee and discussion. As for someone new to the field the lecture selection was almost perfect. The lectures gradually shifted from basic topics to more complex ones. Lectures started with neuron models (HodgkinHuxley, FitzhughNagumo, etc.) and dynamical systems, then to neurophysiology, cable theory (Rall model), oscillators and learning rules, and finishing with memory models (working memory), single neuron computation and plasticity. Moreover, every lecture was followed by a tutorial to apply newly acquired knowledge and as a effect understand it better. I have learned a lot at CAMP and now I know in which direction I want to develop. The second week was dedicated mainly for project work. Projects varied from low level simple neural networks used to classify to more high level systems. I have chosen to build a model in Brian of working memory described in Science article “Synaptic Theory of Working Memory” by Mongillo et al. from 2008. In the end I managed to model a single neuron, but unfortunately there was too little time to properly model the whole network as described in the paper, because of some minor inaccuracies that needed working out. Another very important matter at such events is networking. The staff in charge of CAMP made
sure that the people, both students and lecturers, came from many different backgrounds and prepared a few group activities that helped in bonding. Participants came from medicine, computer science, physics and also various fields of neuroscience. It was a good opportunity to meet young scientists from all over the world. I think that some friendships, that have started during CAMP, will last for many years to come. I hope that I will stay in touch with at least some of people. The course also gave me a chance to speak with researches from leading institutes in the world and hope for some collaboration in the future.
My sincere thanks to INCF for supporting my travel expenses for the NCBS CAMP. We had a wonderful course. We were 30 participants including national and international students and 20-25 wait-listed students were selected for lecture only sessions. The components in the course were well structured, which includes Remedial, Lectures, Tutorials, Discussions and Individual Projects. We got highly qualified faculty around the world to teach us the basis of memory and plasticity, various levels of modeling in computational neuroscience,
sub-cellular electrical and chemical signaling in single neurons. And at network level we studied correlation and ion channel dynamics. How the spiking neuron network learns and memorizes the given patterns of information was one of the highlight of this course. Tutorial session was very helpful for me, it gave us detailed understanding of variety of simulation platform, which includes NEURON, MOOSE, NEST and BRIAN. Why we want to use particular simulator to solve specific research questions was well taught in the tutorials. Discussions were another interesting component of the course. We had hours of chat on computation in brain, parameters and models in Comp Neuro, etc. During the course we had lot of fun, discussing cable theory till 2am, one full day trip to Mysore and an evening trip for DBC,all were unforgettable.During the course of study I did a project on “Studying the effect of stress on hippocampal microcircuit using LFP reconstruction”. Aim of the project was to use a hippocampal neuron model to check if the dendritic atrophy and cellular electrophysiological properties due to stress (Vyas et al., 2002, Narayanan and Chattarji, 2010 ) can explain the change in network activity (LFP, In-vivo) observed at several time points (Ghosh et al., 2013). Adapted version of CA3 PY neuron atrophy model (Narayanan and Chattarji, 2010) was used to study the effect of stress on single neuron field potential. To study the network activity,I built a small detailed network model of CA3 which consist of 100 PY neurons. Stress was induced to the individual neuron models in the network based on (Vyas et al., 2002, Narayanan and Chattarji, 2010) at various levels 0%(control),25%,35% (biologically observed) and 75%.Stimulated these neurons by injecting current through IClamp. LFP was restructured from the network model based on (Holt and Koch 1999, Parasuram et al, 2011). Observed that the amplitude and width of LFP wave get reduced at single neuron level as well as in the population LFP, this can be correlated to the increased evoked activity in hippocampus 1 hour after a single episode of stress. With repeated stress the evoked response comes down to the baseline, this could be because of damage to hippocampal neuron above 35%. I completed this project successfully with the help and input form Shona Chattarji(NCBS), Rishi Narayanan(IISc), Upi Bhalla(NCBS), TA‟s @ CAMP‟14 and Asha, Chaitanya (Amrita Univ.).
I attended the Computational Approaches to Memory and Plasticity (CAMP) Summer School which was conducted at NCBS, Bangalore from 28th June to 12th July 2014. In the Summer school we had lectures which covered the basics of computational neuroscience to the upcoming research topics by eminent scientist like Claudia Clopath, Eve Marder,Stephano Fusi, Upinder S Bhalla, Raghav Rajan, Xiao-Jing Wang, etc. Since I was in tutorials-ve section, it was not a mandatory option to present a mini project during the course. But we had also started with a small project on the memory capacity of pattern classification using perceptron model. We were allowed to attend the all the tutorials which included chemical oscillations, reinforcement learning etc. This course raised my level of understanding in the field of computational neuroscience. I could interact with the different scientist to get more insight into my area of research. The class was also fantastic. Students from different parts of the world who was very enthusiastic and very lively came to attend the course. It was fun being with them too. Overall the course was too informative and enjoyable experience.
Thanks to the support from INCF. I had a chance to meet some of the key scientists in computational neuroscience and discuss my research. At the summer school, we had few tutorials which were very helpful in jump starting our understanding both theoretically as well as practically through hands-on sessions on simulation and modelling. Some of the high-quality lectures delivered by Xiao-Jing Wang, Upinder Bhalla, Claudia Clopath, Sumantra Chatterji, Rishikesh Narayanan, Arthur Wingfield, Eve Marder, Michael Hausser on working memory, chemical networks, learning rules, single synapses & plasticity, single cell plasticity, homeostasis of neurons and networks and dendritic computations proved to be more than useful in our area of research work. Complementing these lectures were the tutorials (dynamical systems, memory capacity, correlations, single neuron computations, etc.,) which went hand in hand adding more practicality to the summer school. This course facilitated exposure to some of the cutting edge research activities as well as establish new friendships with the fellow participants. Learning and fun went together and I am very glad to be part of this excellent summer school.
Activities: CAMP @ Bangalore was an intensive 15-day summer school on the theory and simulation of learning, memory and plasticity in the brain. We were around 50 participants in total (30 full-time, with the rest only attending the lectures) from various backgrounds. The course began with remedial tutorials on the basics of neuroscience, dynamical systems and Python. The speakers (Upinder Bhalla, Sumantra Chattarji, Xiao-Jing Wang, Suhita Nadkarni, Michael Hausser, Eve Marder, Rishikesh Narayanan, Arthur Wingfield, Claudia Clopath, Arvind Kumar, Stefano Fusi, Raghav Rajan) covered a wide range of topics ranging from sub-cellular electrical and chemical signaling in neurons, to micro-circuits and networks, all with an emphasis on learning, memory and plasticity. Hands-on tutorials, held in the afternoons and evenings, were instrumental in giving us a clearer understanding of the topics that had been covered. They were also an excellent way of getting us acquainted with software such as Brian, MOOSE, NEURON and CellBlender. We also had research talks by the invited speakers in the afternoons, and discussions some evenings. In the second week, we also worked on a short project in collaboration with one of the faculty members, that we presented at the very end of the summer CAMP.
With another CAMP participant, I managed to do a project in a few days, under the supervision of Suhita Nadkarni, where we investigated “Frequency dependencies in astrocyte-mediated signal transmission”. Our results were presented on the last day of the summer school. It was a very positive learning experience, during which I gained a much-needed overview of the field of Computational Neuroscience. Since I now have a clearer idea of the field and the level at which I would like to study the brain, I believe it will be easier to make an informed decision about my next career move. I would like to thank the INCF for supporting me in this venture.