Curator Dashboard

A web-based publication of virtually all MIT course content for free. OCW is open and available to the world and is a permanent MIT activity. Materials include free lecture notes, exams, and videos from MIT. No registration required. MIT OpenCourseWare is a free publication of MIT course materials that reflects almost all the undergraduate and graduate subjects taught at MIT. * OCW is not an MIT education. * OCW does not grant degrees or certificates. * OCW does not provide access to MIT faculty. * Materials may not reflect entire content of the course. A site overview is available for MIT OpenCourseWare. You can also browse courses by department or use the advanced search to locate a specific course or topic. High school students and educators should check out Highlights for High School.

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• SciCrunch
• 15 years ago - by Anonymous

Resource Discovery System is a web-accessible and searchable inventory of biomedical research resources. Powered by the Resource Discovery System (RDS) that includes a standards-based informatics infrastructure * Biositemaps Information Model * Biomedical Resource Ontology Extensions * Web Services distributed web-accessible inventory framework * Biositemap Resource Editor * Resource Discovery System Source code and project documentation to be made available on an open-source basis. Contributing institutions: University of Pittsburgh, University of Michigan, Stanford University, Oregon Health & Science University, University of Texas Houston. Duke University, Emory University, University of California Davis, University of California San Diego, National Institutes of Health, Inventory Resources Working Group Members

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• SciCrunch
• 15 years ago - by Anonymous

Command-line software tools for processing biological sequencing data. Barcode demultiplexing, adapter trimming, etc. Primarily written to support an Illumina based pipeline - but should work with any FASTQs.

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• SciCrunch
• 13 years ago - by Anonymous

An interactive reference atlas providing a systematic overview of cyto- and chemoarchectonical features of the hippocampus proper, fasciola, and associated parahippocampal cortices. This atlas system has been developed to serve the need to integrate detailed descriptions of structures and criteria defining boundaries and atlas images in which the underlying histological features can be explored. Features * Alphabetical and hierarchical overview of 18 hippocampal structures * Detailed, illustrated descriptions of 63 boundaries * Interactive image repository with ~100 coronal histological images stained for NeuN, calbindin, and parvalbumin * Triple image viewer in which differently stained neighboring sections can be interactively compared * Graphical overlay of substructures based on described boundary criteria * Bidirectional links between structure descriptions and image repository The atlas is based on histological material from an adult Long Evans rat, stained for NeuN, calbindin, and parvalbumin. The system is intended for researchers working in the field, as well as students interested in this brain region. The atlas is accessed through the structure index or image viewer. Re-use of data from this repository is allowed provided that reference is given to the publication.

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• SciCrunch
• 15 years ago - by Anonymous

Starlab''s mission is to transform science into technologies with a profound and positive impact on society. We achieve this by identifying social needs and the market opportunities they create. Then we reach to science and engineering to propose or provide technical solutions, products and services for governments, industry and downstream markets. Starlab Research carries out interdisciplinary R&D focusing on two areas: Space and Applied Neuroscience. Our vision is to make science more useful, alive, vibrant, faster. Our staff consists of a team of scientists, engineers and economists from different nationalities working together to provide our clients with breakthrough technologies that create business opportunities. The growing Starlab team (now more than 28 on staff) includes 5 nationalities spanning knowledge in physics, engineering, oceanography, computer science, neuroscience and economics. Circa 50% of our staff have a PhD, and more than 80% a Master or PhD. We target technology and applications: the development of new sensors and efficient algorithms to extract information from data, identification of platforms and deployment opportunities, as well as the development of services and products. Interdisciplinarity is a key aspect of our research. Space R&D develops payloads, algorithms and mission feasibility studies. We have demonstrated experience in GNSS technologies, radar altimetry and space astronomy. Earth Observation applications include technologies such as GNSS-R, SAR and multi-spectral analysis for environmental and energy applications. We have demonstrated expertise in the development of innovative sensors and systems in both the Space and Applied Neuroscience areas, signal-processing algorithms, with a strong specialization in electrophysiology algorithms, software and hardware. It will also manage the project and prospect potential commercial impact.

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• SciCrunch
• 15 years ago - by Anonymous

A comparative genome analysis tool for detailed comparison of closely related bacterial-sized genomes. It visualizes precomputed pairwise genome alignments on both dotplot and alignment viewers. Users can add information on this alignment, such as existence of tandem repeats or interspersed repetitive sequences and changes in codon usage bias, to facilitate interpretation of the observed genomic changes. Besides visualization functionalities, it also provides a general framework to process genome-scale alignments using various existing alignment programs. CGAT employs a client-server architecture, which consists of AlignmentViewer (client; a Java application) and DataServer (a set of Perl scripts). The DataServer package contains data construction scripts and CGI scripts and the AlignmentViewer program visualizes the alignment data obtained from the server thorough the HTTP protocol.

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• SciCrunch
• 13 years ago - by Anonymous

HC2 is an EU funded project that aims to promote, support and help define future lines of research in Human Computer Confluence (HCC). HCC is the study of the intersection of HCI, Cognitive Neuroscience, VR/AR, Presence, Pervasive Computing and how they can enable new forms of sensing, perception, interaction and understanding. In a sense it is the study of the disappearing interface. HCC, Human-Computer Confluence, is an ambitious research program studying how the emerging symbiotic relation between humans and computing devices can enable radically new forms of sensing, perception, interaction, and understanding. The horizontal character of HCC makes it a fascinating and fertile interdisciplinary field, but it can also compromise its growth, with researchers scattered across disciplines and groups worldwide. To address this we are building a community of HCC researchers. There are lots of ways you can join in. Add your name to the HCC Players Map, take advantage of our Exchange Program to work with colleagues at your favorite lab, sign up for our Summer School or just follow us on Twitter and LinkedIn to see what''s happening. In order to foster interdisciplinary research and promote HCC research we have set up an Exchange Program. Students that wish to apply for financial support from our Exchange Program should follow the steps provided. The Exchange Program is open to all graduate students (Masters and PhD). A maximum of 500 Euro support will be provided per student.

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• SciCrunch
• 15 years ago - by Anonymous

Software program that provides separate results for TDT, S-TDT, and the combined (overall) test, as appropriate. (entry from Genetic Analysis Software)

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• SciCrunch
• 14 years ago - by Anonymous

Open-source software package for the analysis of neural data. Chronux routines may be employed in the analysis of both point process and continuous data, ranging from preprocessing, exploratory and confirmatory analysis. The current release is implemented as a MATLAB library. Chronux offers several routines for computing spectra and coherences for both point and continuous processes. In addition, it also offers several general purpose routines that were found useful such as a routine for extracting specified segments from data, or binning spike time data with bins of a specified size. Since the data can be continuous valued, point process times, or point processes that are binned, methods that apply to all these data types are given in routines whose names end with ''''c'''' for continuous, ''''pb'''' for binned point processes, and ''''pt'''' for point process times. Thus, mtspectrumc computes the spectrum of continuous data, mtspectrumpb computes a spectrum for binned point processes, and mtspectrumpt compute spectra for data consisting of point process times. Hybrid routines are also available and similarly named - for instance coherencycpb computes the coherency between continuous and binned point process data.

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• SciCrunch
• 17 years ago - by Anonymous

TomatEST DB is a collection of tomato EST sequences downloaded from dbEST. Gene indices are created by grouping overlapping EST sequences into clusters. Each cluster corresponds to a unique gene. A cluster can consist in one or multiple contigs. In the case of a cluster of multiple contigs each contig share similarities with the others in the cluster because of i) putative alternative transcription; ii) paralogy; iii) domain sharing.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 24, 2017.<br/><br/>Platform to enable dissemination of scientific findings, foster open peer commentary and promote collaboration among the research community. Widespread participation in OneLab will increase the quality, transparency and reproducibility of data thus accelerating the pace of scientific discoveries. The result will be a streamlined process from the bench to the clinic with tremendous benefits for the well-being of the general public. OneLab is a private professional network that mirrors the hierarchy of real world research laboratories. Users are designated as either principal investigators (PI) or lab members. PIs can invite lab members to join and data posted by lab members cannot be shared without PI approval. In this way the PI retains FULL CONTROL over the dissemination of scientific content thus safeguarding the primacy of authorship. This professional network will serve as a backdrop for sharing scientific findings, promote collaborations, and provide a basis for open peer commentary. Semantic Search of Structured Content OneLab implements a powerful search functionality that is based on structured content. Users describe their Single Figure Posts (SFPs) using defined fields such as model organism, genes, proteins and assay. This additional layer of structure provides the basis for a smarter and more accurate search engine that understands searcher intent and therefore generates more relevant results. Structured content allows OneLab to go one step further by offering recommendations based on similarities that might not be intuitive, thus increasing potential collaborations among scientists., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 15 years ago - by Anonymous

Phospho3D is a database of three-dimensional structures of phosphorylation sites which stores information retrieved from the phospho.ELM database and which is enriched with structural information and annotations at the residue level. The database also collects the results of a large-scale structural comparison procedure providing clues for the identification of new putative phosphorylation sites.

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• SciCrunch
• 17 years ago - by Anonymous

BioOntology.ch is a blog on the interlinked bio-ontologies for knowledge-based data-driven science. * Bio-ontology is standards: Modern research generates data at unprecedented rates. Where such data are described and labelled using unconstrained text, different terminology is often used for similar or identical things. Such terminological variance is normal and reflects natural language; usually humans have no difficulty resolving ambiguous usages of terminology and discrepant labels. However, due to the sheer volumes of research data being generated, it is necessary to develop computational methods of aggregating and aligning like with like. One approach to addressing this issue is to adopt shared standards for the categorisation of data. Agreement in annotation across different databases increases the value of a standardised terminology, allowing for easier cross-domain integration and querying. * Bio-ontology is knowledge representation: Modern biomedical ontologies harness the formal semantics underlying the Web Ontology Language (OWL), which allows complex logical expressions to be built that define knowledge about the domain, in such a fashion that computers can perform automatic reasoning for tasks such as hierarchy management and consistency checking / error detection. OWL is based on Description Logics, a family of decidable logical languages optimised for the expression of large-scale terminological knowledge such as is found within large biomedical vocabularies. * Bio-ontology is interdisciplinarity: Increasingly, research in the life sciences needs to integrate knowledge and results from multiple disparate fields and methodological approaches in order to gain insight into underlying biological mechanisms. This is the case, for example, when studying the genetic and epigenetic factors in understanding behavioural phenotypes, or in the development of predictive models to enable personalised and translational medicine. Research results from diverse disciplines such as genetics, molecular biology, physiology, chemistry, psychology and medicine have to be integrated in order to build a coherent picture of what is known in order to address key research gaps.

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• SciCrunch
• 15 years ago - by Anonymous

A Brachypodium distachyon comparative genomics resource offering a genome browser, BLAST server, download capabilities, Brachypodium physical map, Comparative maps, and comparison with rice and Sorghum chromosomes. * Genome browser >>> Browse the v1.0 genome assembly and the v1.0 gene predictions from JGI/MIPS. Also displays JIC FST data (T-DNA lines) and alignments of ESTs from wheat, barley and Brachypodium. * BLAST server >>> BLAST your sequences against the Brachypodium sequence assembly and the predicted proteome. * Download sequence >>> Download sequence from the brachy assembly (limited to 50kb regions). Download complete assembly file as FASTA. Download sequence and additional data from the v1.0 annotated assemblyincluding protein-coding sequences as FASTA, translated coding sequences as FASTA, gene sequences as FASTA, and COS markers. PLEASE NOTE: The published genome analysis is based on the v1.0 annotation. The v1.2 annotation can be downloaded from MIPS. * Brachypodium physical map >>> Brachypodium physical map data displayed using SyMAP. (view in genome browser) * Comparative maps >>> Brachypodium genetic and physical maps aligned to rice and wheat. * Comparison with rice and Sorghum chromosomes >>> Dotplots of the Brachypodium assembly aligned to rice and Sorghum chromosomes.

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• SciCrunch
• 15 years ago - by Anonymous

A software program to identify artificial duplicates from raw 454 sequencing reads, including exact duplicates and near identical duplicates.

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• SciCrunch
• 13 years ago - by Anonymous

The tmRDB is a tool in the study of the structures and functions of the tmRNA (earlier called 10S RNA). As the name implies, tmRNA has properties of tRNA and mRNA combined in a single molecule. The tmRDB provides aligned, annotated and phylogenetically ordered tmRNA sequences. The alignments of the sequences represent conserved secondary structure elements where each base pair is proven by comparative sequence analysis. Where possible, we established direct links to primary sources. We acknowledge support provided by the National Institutes of Health and the Danish Technical Research Council. tRNA, mRNA, trans-translation, rescue, ribosome, broken mRNA, bacteria, mitochondria chloroplasts, cyanelles, bacteriphage, phylogenetic

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• SciCrunch
• 17 years ago - by Anonymous

A collection of amino acid sequences for all the completed genomes and the annotated trans beta-barrel membrane proteins (TMBs) using different discrimination algorithms. For each genome, the calculations have been performed with statistical methods and machine learning techniques and the results are accumulated in the database. TMBETA-GENOME has the feasibility of selecting the organism from the three kingdoms of life, archaea, bacteria and eukaryote. Further, users have the option to select any of the methods or their combinations, and display the results with/without amino acid sequence information.

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• SciCrunch
• 17 years ago - by Anonymous

The mission of AIDS.ORG is to help prevent HIV infections and to improve the lives of those affected by HIV and AIDS by providing education and facilitating the free and open exchange of knowledge at an easy-to-find centralized website. AIDS.ORG makes access to important AIDS information easier and faster. We provide prevention, testing, and treatment information currently to well over 4 million people a year. AIDS.ORG has been awarded the Health on the Net Foundation Code of Conduct (HONcode) seal for reliability and credibility of information in the field of healthcare. Additionally, every year over 2.4 million young people under the age of 25 turn to AIDS.ORG, making us an important resource since over 50% of all new HIV infections in the USA occur in this age group. AIDS.ORG, Inc. is a nonprofit 501(c) (3) educational organization, and maintains a very strict privacy policy. We make it our goal to be the best starting point for someone looking for AIDS information on the Internet. Our intent is that users be directed to the best information on the topic they''re investigating. We bring people together to share knowledge and experiences. In the past, we also provided the very first Internet-based program of accredited AIDS education for medical professionals, allowing doctors in rural and isolated areas to better serve AIDS patients.

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• SciCrunch
• 15 years ago - by Anonymous

An Software resource

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• SciCrunch
• 13 years ago - by Anonymous

Software tool as collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.

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• SciCrunch
• 13 years ago - by Anonymous