Some of my python tools for computational neuroscience - michaelerule/neurotools

NeuroTools provides custom viral vectors tailored for neuroscience experiments. We offer small prep sizes of AAV, Lentivirus, HSV, and Rabies at competitive rates for the neuroscience community.

WZ Biosciences are specialized in design and preparing viral based vectors in gene delivery for research and gene therapy purpose. We have many products and services. Our plasmid products include more...

Title: Neuroscience Data: Visualize, Collaborate & Build Author: Dr. Stephen Larson Time: July 20, 2018: 11 AM PST/ 2 PM EST Synopsis: The modern neuroscience researcher or neurotech company faces a challenging landscape in order to use experimental or device data to its maximal potential. While data collection and accumulation are expanding, approaches to data management and insight gathering still fall short. In this free, open webinar we’ll be discussing how three major activities - 1) visualize, 2) collaborate, and 3) build - can massively expand an organization's ability to extract value from neuroscience data and work with it on the internet. The webinar (45 mins + Q&A) will feature online interfaces and showcase the technological landscape available to solve this challenge and drive the neuroscience research industry forward.

The Neuroscience Information Framework Presents this week's NeuroTools Webinar on June 29th, 2018: Title: IEDB Analysis Resource – Package Of Tools For Immune Epitope Prediction And Analysis RRID: Immune Epitope Database and Analysis Resource (RRID:SCR_006604) : https://scicrunch.org/resources/Tools/record/nlx_144509-1/SCR_006604/resolver?q=*&l=&sort=internal_create_date Presenter: Dr. Sinu Paul Biography: Dr. Sinu Paul is a bioinformatics scientist at the Immune Epitope Database and Analysis Resource Project located at the La Jolla Institute for Allergy & Immunology in San Diego, California. His work is mainly focused on development of computational algorithms and tools using machine learning techniques and statistical applications for application in immunology such as immune epitope prediction and analysis of epitope related data. Synopsis of Webinar: The IEDB Analysis Resource (IEDB-AR, http://tools.iedb.org) hosts a collection of tools for the prediction and analysis of immune epitopes. Epitopes are peptides derived from antigens and recognized by T cells which in turn result in generation of immune response. Identification of epitopes is important in several areas such as vaccine discovery, development of diagnostics and removal of unwanted immune responses against protein therapeutics. Experimental identification of epitopes can be laborious and time consuming. Therefore computational prediction tools are used nowadays to select epitope candidates. The IEDB-AR provides several methods for prediction of MHC class I and MHC class II binding affinity, antigen processing, immunogenicity and B cell epitopes as well as tools for analysis of epitope related data. The talk will give an overview of important tools available at IEDB-AR and brief descriptions on how to use them and interpret the results. Related Links: IEDB Analysis Resource: http://tools.iedb.org/main/ This webinar is part of the Neuro-Tools Webinar series, for upcoming webinars please visit The Neuroscience Information Framework: https://neuinfo.org/about/UpcomingWebinars

Title: The Immune Epitope database and Analysis Resource RRIDs: The Immune Epitope database and Analysis Resource (RRID:SCR_006604) : https://scicrunch.org/resources/Tools/record/nlx_144509-1/SCR_006604/resolver?q=*&l=&sort=internal_create_date National Institute of Allergy and Infectious Diseases (RRID:SCR_012740) : https://scicrunch.org/resources/Tools/record/nlx_144509-1/SCR_012740/resolver?q=NIAID&l=NIAID Presenter: Dr. Randi Vita Dr. Vita is the Lead Ontology and Quality Manager at The Immune Epitope Database and Analysis Project located at the La Jolla Institute for Allergy & Immunology in San Diego, California. She has spent the past 12 years involved in the curation of immunological data, the design and implementation of the IEDB database and website, and the integration of ontologies into the IEDB and other related projects. Her primary focus has been the use of ontologies to standardize data capture, facilitate interoperability between projects, and generate data validation. Synopsis of Webinar: The Immune Epitope Database (IEDB) (http://www.iedb.org) is a freely available, widely used bioinformatics resource sponsored by the NIAID. The IEDB catalogs all epitopes for humans, non-human primates, rodents, and any other studied vertebrate derived from allergens, infectious diseases, autoantigens, and transplantation antigens. Our data includes more than 1.5 million experiments derived from more than 19,000 publications. The IEDB also includes epitope prediction tools to accelerate immunology research around the world. In the webinar, Dr. Vita will give an overview of the IEDB, including where the data come from, how they are entered, structured, and retrieved, and how they can be used to further immunological research. This webinar is part of the Neuro-Tools Webinar series, for upcoming webinars please visit The Neuroscience Information Framework: https://neuinfo.org/about/UpcomingWebinars

The Neuroscience Information Framework Presents this week's NeuroTools Webinar on April 27th, 2018: Title: Mouse Phenome Database (RRID:SCR_003212): An Integrative Database And Analysis Suite For Curated Empirical Phenotype Data, RRID: https://scicrunch.org/resolver/SCR_003212 Presenters: Dr. Molly Bogue And Dr. Elissa Chesler Biographies: Dr. Molly Bogue is a Research Scientist at The Jackson Laboratory in Bar Harbor, Maine. She is Principal Investigator of the Mouse Phenome Database project. Her interests include research replicability in preclinical research and sex differences. Dr. Elissa Chesler is currently an Associate Professor of Bioinformatics and Computational Biology at The Jackson Laboratory in Bar Harbor, Maine. She holds a Doctor of Philosophy in Neuroscience from the University of Illinois at Urbana-Champaign. Her laboratory integrates quantitative genetics, bioinformatics and behavioral science to understand and identify the biological basis for the relationships among behavioral traits. Synopsis of Webinar: The Mouse Phenome Database (MPD), in existence since 2001, provides access to primary experimental trait data, genotypic variation, protocols and analysis tools for mouse genetic studies. Data are contributed by investigators worldwide and represent a broad scope of phenotyping endpoints and disease-related traits in naïve mice and those exposed to drugs, environmental agents or other treatments. MPD ensures rigorous curation of phenotype data and supporting documentation using relevant ontologies and controlled vocabularies. As a repository of curated and integrated data, MPD provides a means to access/re-use baseline data, as well as allows users to identify sensitized backgrounds for making new mouse models with genome editing technologies, analyze trait co-inheritance, benchmark assays in their own laboratories, and many other research applications. MPD’s primary source of funding is NIDA. For this reason, a majority of MPD data is neuro- and behavior-related. In this webinar, we will explore new tools and features of the recently re-implemented MPD with emphasis on neuro-behavior examples. Related Links: Mouse Phenome Database: https://phenome.jax.org This webinar is part of the Neuro-Tools Webinar series, for upcoming webinars please visit The Neuroscience Information Framework: https://neuinfo.org/about/UpcomingWebinars

The Neuroscience Information Framework Presents this week's NeuroTools Webinar on April 6th, 2018: Title: GeneWeaver (RRID:SCR_003009): A System For The Integration And Analysis Of Heterogeneous Functional Genomics Data RRID: https://scicrunch.org/resolver/SCR_003009 Presenters: Dr. Elissa J. Chesler And Dr. Erich J. Baker Biographies: Dr. Elissa J. Chesler: Dr. Chesler is a professor at The Jackson Laboratory in Bar Harbor, Maine, where she works on the development of tools and resources for integrative genetics and genomics with an emphasis on their application in behavioral genetics. She is the Director of the NIDA Center for Systems Neurogenetics of Addiction and has led the GeneWeaver project since its inception in 2006 as “The Ontological Discovery Environment”. Dr. Erich J. Baker: Dr Baker is a professor of Computer Science at Baylor University. He has been involved in the development of the GeneWeaver web application since its inception. Synopsis of Webinar: GeneWeaver is a web application for the integrated cross-species analysis of functional genomics data to find convergent evidence from heterogeneous sources. The application consists of a large database of gene sets curated from multiple public data resources and curated submissions, along with a suite of analysis tools designed to allow flexible, customized workflows through web-based interactive analysis or scripted API driven analysis. Gene sets come from multiple widely studied species and include ontology annotations, brain gene expression atlases, systems genetic study results, gene regulatory information, pathway databases, drug interaction databases and many other sources. Users can retrieve, store, analyze and share gene sets through a graded access system. Analysis tools are based on combinatorics and statistical methods for comparing, contrasting and classifying gene sets based on their members. An overview of the database and tools will be presented along with applications in alcohol and addiction biology. GeneWeaver is supported by NIH R01 AA18776, jointly funded by NIDA and NIAAA. Additional support comes from the Center for Precision Genetics, NIH U54 OD 020351. This webinar is part of the Neuro-Tools Webinar series, for upcoming webinars please visit The Neuroscience Information Framework: https://neuinfo.org/about/UpcomingWebinars

The Neuroscience Information Framework is a dynamic inventory of Web-based neuroscience resources: data, materials, and tools accessible via any computer connected

The Neuroscience Information Framework is a dynamic inventory of Web-based neuroscience resources: data, materials, and tools accessible via any computer connected

The Neuroscience Information Framework Presents this week's NeuroTools Webinar on March 2nd, 2018: Title: DataLad (RRID:SCR_003931) - Decentralized Distribution And Management Of Scientific Datasets RRID: https://scicrunch.org/resolver/SCR_003931 Presenter: Dr. Yaroslav O. Halchenko: Currently the Research Assistant Professor at Psychology and Brain sciences department at Dartmouth, leading the Center for Open Neuroscience, Dr. Yaroslav O. Halchenko holds a Ph.D. in Computer Science from the New Jersey Institute of Technology and got post-doctoral training at Dartmouth College. He is a neuroimaging research scientist, an official Debian developer, a member of INCF neuroimaging task force, and a lead of PyMVPA, NeuroDebian, DataLad and other projects. With the goal of contributing to our understanding of the brain function, Dr. Halchenko is interested in developing new and formalizing existing analysis methodologies and software solutions in the domain of computational and cognitive neuroscience. Synopsis of Webinar: DataLad (http://datalad.org/) is ongoing work funded by NSF and German BMBF, to adapt the model of open-source software (OSS) distributions to address the technical limitations of today's data-sharing and to provide all components of a "data distribution" and "data management platform". The key concepts are: 1) Leverage - but do not replace - independent, existing, and future data hosting solutions to form a federated platform for data-sharing. 2) Employ software for data tracking and deployment logistics specialized for large data (git-annex) built atop Git, the most capable distributed version control system (dVCS) available today, to enable efficient data access at any level of granularity (from single files to entire collections of datasets). DataLad provides access to data available from various sources (e.g. lab or consortium web-sites such as INDI; data sharing portals such as openfmri.org (http://openfmri.org/) and crcns.org (http://crcns.org/)) through a single interface. It enables students and scientists to operate on data using familiar concepts, such as files and directories, while transparently managing data access and authorization with underlying hosting providers. File an Issue about a bug or source code: https://github.com/datalad/datalad General Neuroscience Questions: https://neurostars.org/latest Crystal Clear version of Recorded Part of webinar: https://www.youtube.com/watch?v=sDP1jhRkKRo This webinar is part of the Neuro-Tools Webinar series, for upcoming webinars please visit The Neuroscience Information Framework: https://neuinfo.org/about/UpcomingWebinars

The Neuroscience Information Framework Presents this week's NeuroTools Webinar on February 16th, 2018: Title: Cellosaurus (RRID:SCR_013869) RRID: https://scicrunch.org/resolver/SCR_013869 Presenter: Dr. Amos Bairoch: Amos Bairoch is a Swiss bioinformatician and Professor of Bioinformatics at the Department of Human Protein Sciences of the University of Geneva where he leads the CALIPHO group at the Swiss Institute of Bioinformatics (SIB) combining bioinformatics, biocuration, and experimental efforts to functionally characterize human proteins. Until June 2009, Amos headed the Swiss-Prot group which develops the UniProtKB/Swiss-Prot knowledgebase which he created in 1986 as well as the PROSITE and ENZYME databases. He was also co-responsible for the development of ExPASy, the world's first website dedicated to protein molecular biology. Currently his main activities are focused on the development of neXtProt, a web knowledge platform on human proteins and of the Cellosaurus. Amos Bairoch has been awarded several distinctions, among which the European Latsis Prize, the Otto Naegeli Prize and the HUPO Distinguished Achievement Award. He is an ISCB Fellow. Synopsis of Webinar: The Cellosaurus (RRID:SCR_013869) (https://web.expasy.org/cellosaurus/) is a knowledge resource on cell lines. The aim of this webinar is to describe the content of the Cellosaurus but also to discuss some issues mundane to cell lines especially misidentification/contamination, naming problems as well the lack of standardization of the information reported by cell line collections/companies. We will also describe our collaboration with ICLAC (http://iclac.org/) and our involvement in the Resource Identification Initiative (https://www.force11.org/group/resource-identification-initiative). Contact Information: email: cellosaurus@sib.swiss Twitter: @cellosaurus This webinar is part of the Neuro-Tools Webinar series, for upcoming webinars please visit The Neuroscience Information Framework: https://neuinfo.org/about/UpcomingWebinars

The Neuroscience Information Framework Presents this week's NeuroTools Webinar on January 19th, 2018: Title: Introducing The NIDA Core Center Of Excellence In Omics, Systems Genetics, And The Addictome Presenter: Dr. Rob Williams: Robert (Rob) W. Williams received a BA in neuroscience from UC Santa Cruz (1975) and a Ph.D. in physiology at UC Davis with Leo M Chalupa (1983). He did postdoctoral work in developmental neurobiology at Yale with Pasko Rakic and moved to the University of Tennessee in 1989. He is chair of the Department of Genetics, Genomics and Informatics at UTHSC. Williams holds the UT Oak Ridge National Laboratory Governor’s Chair in Computational Genomics. He was a past president of the International Society for Behavioural and Neural Genetics and founding director of the Complex Trait Community (www.complextrait.org). He is editor-in- chief of Frontiers in Neurogenomics, and serves on the editorial boards of Genes, Brain & Behavior, Neuroinformatics, Mammalian Genome, Molecular Vision, European Journal of Anatomy, Alcohol, BiomedCentral Neuroscience, the Journal of Biomedical Discovery and Collaboration, and Behavior Genetics. One of Williams’ more notable contributions is in the field of systems genetics and expression genetics (eQTL analysis). He and his research group have built GeneNetwork (www.genenetwork.org), an online resource and suite of gene mapping code that is used widely by the genetics and molecular biology communities. Synopsis of Webinar: Technical and computational barriers prevent researchers and clinicians from incorporating more powerful genomic methods in addiction research. The purpose of the new NIDA P30 Core Center of Excellence in Omics, Systems Genetics, and the Addictome is to empower researchers to analyze genetic, epigenetic and environmental causes of drug abuse risk, relapse, and treatment. We are doing this by assembling many omics resources—primarily for rat, mouse and human—that can give investigators mechanistic and behavioral insights into addiction. In addition, we provide local workshops in systems genetics and advanced computational/statistical modeling for NIDA research teams. Links: http://www.genenetwork.org/ (RRID:SCR_002388: https://scicrunch.org/resolver/SCR_002388) http://www.complextrait.org/ Useful Publications: 1. How to use GeneNetowkr: Mulligan MK, Mozhui K, Prins P, Williams RW (2017) GeneNetwork: A Toolbox for Systems Genetics. In Systems Genetics, Methods in Molecular Biology 1488:75-120 [An updated primer in using GeneNetwork for molecular analysis of mouse and human cohorts.] PDF version: http://www.genenetwork.org/images/upload/Mulligan_How_To_Use_GeneNetwork_2017_v1.pdf PubMed access: https://www.ncbi.nlm.nih.gov/pubmed/27933521 2. Resources for Systems Genetics: Williams RW, Williams EG (2017) Resources for Systems Genetics. In Systems Genetics, Methods in Molecular Biology 1488:3-29. [This review is intended to help you when making the hard choices about types of resources to use in system genetic studies. The short answer: embrace diversity in your resources. The computational barriers to joint analysis are now minimal.] PDF version: http://www.genenetwork.org/images/upload/Williams_ResourcesSystemsGenetics_MethodsMolBio_2016.pdf This webinar is part of the Neuro-Tools Webinar series, for upcoming webinars please visit The Neuroscience Information Framework: https://neuinfo.org/about/UpcomingWebinars

The Neuroscience Information Framework Presents this week's NeuroTools Webinar on December 8th, 2017 Title: Hypothes.is (RRID:SCR_000430): Creating A Light-Weight, Open, Portable Knowledge Layer Over Biomedicine RRID: https://scicrunch.org/resolver/SCR_000430 Presenter: Dr. Maryann Martone: Maryann Martone received her BA from Wellesley College in Biological Psychology and Ancient Greek and her Ph. D. in Neuroscience from the University of California, San Diego. She is a professor Emerita at UCSD, but still maintains an active laboratory She started her career as a neuroanatomist, specializing in light and electron microscopy, but her main research for the past 15 years focused on informatics for neuroscience, i.e., neuroinformatics. She led the Neuroscience Information Framework (NIF), a national project to establish a uniform resource description framework for neuroscience, and the NIDDK Information Network (dknet), a portal for connecting researchers in digestive, kidney and metabolic disease to data, tools, and materials. She is Editor-in-Chief of Brain and Behavior, an open access journal, and on the editorial board of Nature Scientific Data, Frontiers in Neuroinformatics and Journal of Neuroinformatics. Dr. Martone is past President of FORCE11, an organization dedicated to advancing scholarly communication and e-scholarship and currently serves as the chair of the Council on Training, Science and Infrastructure for the International Neuroinformatics Coordinating Facility. Since retiring, she has served as the Director of Biological Sciences for Hypothesis, a technology non-profit developing an open annotation layer for the web and founded SciCrunch, a technology start up based on technologies developed by NIF (RRID:SCR_002894: https://scicrunch.org/resolver/SCR_002894) and dkNET (RRID:SCR_001606: https://scicrunch.org/resolver/SCR_001606) . Synopsis of Webinar: Annotation -- from personal note-taking to structured knowledge creation -- is fundamental to biomedicine. Hypothes.is (https://web.hypothes.is/) (RRID:SCR_000430) has developed the capability to add interactive and machine-searchable annotations to any web resource. Annotation, particularly scholarly annotation, is distinct from current commenting systems in that it is anchored to a specific portion of a research object, i.e., a statement, an object in an image, a gene sequence and located according to the physical particulars of the target, i.e., the margin, image coordinates. Web annotation provides a powerful new capability to biomedicine. With Hypothes.is, any content on the web can be turned into an interactive forum for on-line discussions or annotated with additional information. Because Hypothes.is is engineered for the web, annotations can be replied to, shared and searched across contexts. Hypothesis supports public, private and group annotation. The implications of this technology are profound for collaborative creation of knowledge across many domains, including journalism, government, education and research. In biomedicine, Hypothes.is provides an independent communication channel on top of the scientific literature where additional information can be added to otherwise static artifacts. It provides a lightweight interactive tool for peer review, education and biocuration. Annotations are tied to article DOI’s, so that annotations will sync across the same article in different locations, e.g., the publisher’s web site, a pdf and Pub Med Central. Through direct linking, annotations can be shared, and the recipient will be taken directly to the annotation in context. Through these capabilities, Hypothesis is laying the foundation for next generation referencing systems. In this presentation, I provide an overview of the technology and show how Hypothesis is being used within biomedicine. This webinar is part of the Neuro-Tools Webinar series, for upcoming webinars please visit The Neuroscience Information Framework: https://neuinfo.org/about/UpcomingWebinars