aspuru-list February 2008

aspuru-list@lists.fas.harvard.edu

19 participants
53 discussions

[Aspuru-Guzik group list] Update: George Schatz

by Patrick Rebentrost

Dear Group, latest update on the visit of George Schatz. The meeting is Thursday, 7 Feb, at 2:45 p.m. in Naito 30 (near Bauer cafe). We will only have 25 minutes, since he is delayed due to a snow storm in Chicago. By the way, his Nature paper from last week can be found here: http://www.nature.com.ezp1.harvard.edu/nature/journal/v451/n7178/full/natur… Best, Patrick

16 years, 2 months

[Aspuru-Guzik group list] [iic-seminars] IIC Internships

by Helene Tingle

The IIC is reviewing resumes for summer internships. Please submit your resumes with a cover letter stating your area of research. Interested students may check the URL below. http://iic.harvard.edu/employment/index.html 2008 Summer Internships Astronomical Medicine The Initiative in Innovative Computing at Harvard seeks a qualified intern to implement software algorithms for segmenting and searching for features in cross-discipline scientific imaging. The IIC has several projects that involve classifying, retrieving, and visualizing regions of images that meet particular statistical criteria. These projects include a medical imaging/astronomy collaboration, a time series analysis center, and an effort to segment large amounts of neural tissue from electron microscopy data. This intern would focus intensively on one application domain, the use of the open-source Insight Toolkit (ITK) for segmentation of astronomy data (potentially including techniques such as statistical classification, interactive editing, and visual display of results), while providing guidance to the rest of IIC on the development of cross-discipline tools and techniques for scientific image segmentation. Image data for this project comes from multiple data channels acquired at different wavelengths, using different instruments, and will be segmented according to intensity-, region-, and shape-based criteria. A successful applicant should have working knowledge of image segmentation algorithms and software frameworks at the Master's Degree level or beyond. Working knowledge of ITK and C++ a strong plus. Experience with developing interactive software tools, visualization applications, or search algorithms also a plus. Design Group The intern will be involved with the development of Drupal-based web sites which will require the student to be familiar with HTML, CSS, PHP. Familiarity with CVS/SVN, Drupal and MySQL and Photoshop is desirable but not necessary. At the end of the summer, it will be possible to show progress on a number of different web sites both internal and external. New features and capabilities will be supported, most notably on the IIC website to support internal documents and workflow. The student will learn best practices in site development and deployment and get experience in HTML, CSS, PHP and Drupal. Connectome The goal of the project is to do research in automatic extraction of axons from electron microscopy images of brain tissue. We will investigate using shape-based surface evolution models for the segmentation of EM volume data of neural tissue. We will develop active contour models using ITK/VTK that searches for tubular structures using Higher Order Active Contours. The model minimizes an energy functional that favors branching cylindrical shapes over others. The intern will develop a new method for automatic extraction of axons in EM volume data. The intern will implement his ideas and algorithms in software. All findings will be properly documented in a final internal report. Tracking axons in EM volume data is one of the key components of the Connectome project and will have substantial impact in neuroscience. Scientist Collaboration Framework Computer science graduate student with experience in web technologies including PHP, AJAX & HTML. Familiarity with emerging Semantic Web technologies such RDF, OWL and triple-stores. Skilled at programming and software development methodologies. Create a semantic module for bibliographies in Drupal (content management system). Such a system would allow easy import/export of bibliographies from external sources (such as EndNote, RefMan or Bibtex) as well as allow the user to easily create a new entry. The framework will allow tagging of the bibliography with keywords from controlled vocabularies. Users of the framework will be able to perform high precision knowledge mining on these bibliographies. Drupal is increasingly being adopted as the content management of choice by scientific communities (e.g. IIC, HSCI). Bibliography maintenance, annotation and mining is one of the challenges for such a web-based community and the goal of this module is to address that challenge. Time Series Center The IIC Time Series Center is collaborating with scientist, computer scientists, and statisticians to develop a-priori algorithms for the discovery of anomalies, similarities and dis-similarities, and patterns in time series. Our research combines work in computer science, astronomy, numerical and symbolic algorithms, web services, and databases. Early classification and early detection of anomalous events in time series. Machine learning techniques such as Support Vector Machine (SVM) and k Nearest Neighbors (kNN) can be applied to classify time series by applying a distance metric. Such techniques have been applied successfully in different fields, e.g. in astronomy to classify periodic stars. In this project we want to explore methods on streaming data for early warning systems. We will apply existing probabilistic classification methods as well as develop new approaches in order to identify automatically anomalous events. Methods that produce high accuracy will be applied to existing data at the Time Series Center. We are looking for a student with a strong background in Computer Science and strong understanding of machine learning and understanding of time series analysis. _______________________________________________ iic-seminars mailing list iic-seminars(a)calists.harvard.edu http://calists.harvard.edu/mailman/listinfo/iic-seminars

16 years, 2 months

[Aspuru-Guzik group list] Fwd: George Schatz

by Patrick Rebentrost

>Due to a major winter storm raging in Chicago, George Schatz's >flight today has been cancelled and he has been rescheduled to a >flight tomorrow morning. > >We hope that he is able to arrive to Harvard by 12:00 noon. > >Updates to follow! > >h. > >Helen L. Schwickrath >Seminar and Events Coordinator >Harvard University >Department of Chemistry and Chemical Biology >12 Oxford Street >Cambridge, MA 02138 >(617) 496-8190 (Voice) >(617) 496-5618 (Fax) >helen(a)chemistry.harvard.edu

16 years, 2 months

[Aspuru-Guzik group list] [iic-seminars] IIC Seminar today - Fran Berman at 4pm

by Helene Tingle

Initiative in Innovative Computing @ Harvard Seminar Series Wednesday, February 6, 2008; 4:00pm 60 Oxford Street, Room 330 Dr. Fran Berman, Director, San Diego Supercomputer Center Professor High Performance Computing Endowed Chair, UC San Diego Seminar Title: De-constructing Cyberinfrastructure Abstract: Cyberinfrastructure, the integrated framework of enabling information and computational technologies, experts, and tools, has emerged as a foundation for applications in the Information Age. The vision of Cyberinfrastructure is powerful and important, yet designing, building, deploying, evaluating, and funding capable, useful, and usable Cyberinfrastructure is a an immense challenge. In this talk, San Diego Supercomputer Center Director Fran Berman discusses the challenges and opportunities of building and deploying Cyberinfrastructure as a continuous bootstrapping process that furthers both scientific progress and technology capability. Upcoming IIC Seminars: Continue to stay up to date with our IIC Seminar Schedule. Parking is available in the 52 Oxford Street Garage. Please tell the attendant that you are attending the IIC Seminar. _______________________________________________ iic-seminars mailing list iic-seminars(a)calists.harvard.edu http://calists.harvard.edu/mailman/listinfo/iic-seminars

16 years, 2 months

[Aspuru-Guzik group list] ACTC

by Alan Aspuru-Guzik

Dear group, If anybody wants to submit a poster for ACTC, let me know. There are competitions for postdoctoral talks as well. http://www.actc.chem.northwestern.edu/index.html -- Alan Aspuru-Guzik Assistant Professor Department of Chemistry and Chemical Biology 12 Oxford Street Harvard University Cambridge, MA 02138 Tel: (617)384-8188 Group URL: http://aspuru.chem.harvard.edu

16 years, 2 months

[Aspuru-Guzik group list] George Schatz, Thursday, 07 Feb

by Patrick Rebentrost

Dear Group, the group has the opportunity to talk to George Schatz (Northwestern) on Thursday from 2:45 p.m. to 3:25 p.m. Please feel free to join! I'll announce the room as soon as I know more. Cheers, Patrick

16 years, 2 months

[Aspuru-Guzik group list] books

by Ali Najmaie

Hello all, Apparently I still owe the Chemistry Library the following four books. Since I returned all the book I had on my desk, I suspect these are books that I either checked out for others in the group or others borrowed from my desk. I would appreciate it if you could return them to the chemistry library and let me know as well. Many thanks, Ali *Handbook of conducting polymers* Skotheim, Terje A QD382.C66 H36 1998 * The theory of open quantum systems* Breuer, Heinz-Peter QC174.85.O6 B74 2002 * Fluorescence imaging spectroscopy and microscopy* Wang, X. F. (Xue Feng) QD96.F56 F57 1996 * Valency and bonding : a natural bond orbital donor-acceptor perspective* Weinhold, Frank QD469 .W45 2005

16 years, 2 months

[Aspuru-Guzik group list] Scientific Word CD

by Masoud Mohseni

Hi All, I am looking for a Scientific Word CD that should be somewhere in the group. Could you please respond to this email if you have it? Thanks, Masoud -- *********************************************************** Masoud Mohseni, Postdoctoral Fellow, Harvard University Department of Chemistry and Chemical Biology 12 Oxford St, Cambridge, MA, 012138, USA Office: M 111, Telephone: (617) 496-9964, Fax: (617) 496-9411 Email: masoud(a)chemistry.harvard.edu URL: http://aspuru.chem.harvard.edu/People/Masoud%20Mohseni/ **************************************************************

16 years, 2 months

[Aspuru-Guzik group list] Las Call

by Roberto Olivares-Amaya

Hi Please send your journal requests to Roberto Sincerely, Roberto On Jan 25, 2008 12:57 PM, Roberto Olivares-Amaya <robolivares(a)gmail.com> wrote: > Hi > This is to remind you to send me the journals list that you think might be > requested. > Best > Roberto > > On Jan 22, 2008 6:25 PM, Roberto Olivares-Amaya <robolivares(a)gmail.com> > wrote: > > > Hi > > As you know, Harvard does not hold a subscription to many of the leading > > journals. Therefore, we're trying to make a list so that the library can > > include them. Send the list to me ( robolivares(a)gmail.com). I'll be > > compiling the list. > > Best regards > > Roberto > > > >

16 years, 2 months

[Aspuru-Guzik group list] [iic-seminars] IIC Seminar Reminder - Fran Berman on Wednesday

by Helene Tingle

16 years, 2 months

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aspuru-list February 2008