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Upload

About: Upload is a(n) research topic. Over the lifetime, 18959 publication(s) have been published within this topic receiving 202014 citation(s).


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Journal ArticleDOI
TL;DR: A significant update to one of the tools in this domain called Enrichr, a comprehensive resource for curated gene sets and a search engine that accumulates biological knowledge for further biological discoveries is presented.
Abstract: Enrichment analysis is a popular method for analyzing gene sets generated by genome-wide experiments. Here we present a significant update to one of the tools in this domain called Enrichr. Enrichr currently contains a large collection of diverse gene set libraries available for analysis and download. In total, Enrichr currently contains 180 184 annotated gene sets from 102 gene set libraries. New features have been added to Enrichr including the ability to submit fuzzy sets, upload BED files, improved application programming interface and visualization of the results as clustergrams. Overall, Enrichr is a comprehensive resource for curated gene sets and a search engine that accumulates biological knowledge for further biological discoveries. Enrichr is freely available at: http://amp.pharm.mssm.edu/Enrichr.

3,882 citations

01 Jan 2003
TL;DR: The BitTorrent file distribution system uses tit-fortat as a method of seeking pareto efficiency, which achieves a higher level of robustness and resource utilization than any currently known cooperative technique.
Abstract: The BitTorrent file distribution system uses tit-fortat as a method of seeking pareto efficiency. It achieves a higher level of robustness and resource utilization than any currently known cooperative technique. We explain what BitTorrent does, and how economic methods are used to achieve that goal. 1 What BitTorrent Does When a file is made available using HTTP, all upload cost is placed on the hosting machine. With BitTorrent, when multiple people are downloading the same file at the same time, they upload pieces of the file to each other. This redistributes the cost of upload to downloaders, (where it is often not even metered), thus making hosting a file with a potentially unlimited number of downloaders affordable. Researchers have attempted to find practical techniqes to do this before[3]. It has not been previously deployed on a large scale because the logistical and robustness problems are quite difficult. Simply figuring out which peers have what parts of the file and where they should be sent is difficult to do without incurring a huge overhead. In addition, real deployments experience very high churn rates. Peers rarely connect for more than a few hours, and frequently for only a few minutes [4]. Finally, there is a general problem of fairness [1]. The total download rate across all downloaders must, of mathematical necessity, be equal to the total upload rate. The strategy for allocating upload which seems most likely to make peers happy with their download rates is to make each peer’s download rate be proportional to their upload rate. In practice it’s very difficult to keep peer download rates from sometimes dropping to zero by chance, much less make upload and download rates be correlated. We will explain how BitTorrent solves all of these problems well. 1.1 BitTorrent Interface BitTorrent’s interface is almost the simplest possible. Users launch it by clicking on a hyperlink to the file they wish to download, and are given a standard “Save As” dialog, followed by a download progress dialog which is mostly notable for having an upload rate in addition to a download rate. This extreme ease of use has contributed greatly to BitTorrent’s adoption, and may even be more important than, although it certainly complements, the performance and cost redistribution features which are described in this paper.

2,951 citations

Patent
20 Mar 1998
Abstract: A method for monitoring client (12) interaction with a resource downloaded from a server (10) in a computer network includes the steps of using a client (12) to specify an address of a resource located on a first server (10), downloading a file corresponding to the resource from the first server (10) in response to specification of the address, using the client (12) to specify an address of a first executable program located on a second server (10), the address of the first executable program being embedded in the file downloaded from the first server (10), the first executable program including a software timer for monitoring the amount of time the client (12) spends interacting with and displaying the file downloaded from the first server (10), downloading the first executable program from the second server to run on the client (12) so as to determine the amount of time the client (12) interacts with the file downloaded from the first server (10). A server (10) for use in analysis and automatically serving out files assembled according to user interests and preferences.

1,516 citations

Journal ArticleDOI
TL;DR: A web tool called ClustVis that aims to have an intuitive user interface for the Principal Component Analysis and heatmap plots and is freely available at http://biit.cs.ut.ee/clustvis/.
Abstract: The Principal Component Analysis (PCA) is a widely used method of reducing the dimensionality of high-dimensional data, often followed by visualizing two of the components on the scatterplot. Although widely used, the method is lacking an easy-to-use web interface that scientists with little programming skills could use to make plots of their own data. The same applies to creating heatmaps: it is possible to add conditional formatting for Excel cells to show colored heatmaps, but for more advanced features such as clustering and experimental annotations, more sophisticated analysis tools have to be used. We present a web tool called ClustVis that aims to have an intuitive user interface. Users can upload data from a simple delimited text file that can be created in a spreadsheet program. It is possible to modify data processing methods and the final appearance of the PCA and heatmap plots by using drop-down menus, text boxes, sliders etc. Appropriate defaults are given to reduce the time needed by the user to specify input parameters. As an output, users can download PCA plot and heatmap in one of the preferred file formats. This web server is freely available at http://biit.cs.ut.ee/clustvis/.

1,483 citations

Journal ArticleDOI
TL;DR: A Galaxy based web server for processing and visualizing deeply sequenced data, called deepTools, that enables users with little bioinformatic background to explore the results of their sequencing experiments in a standardized setting and can be used without registration.
Abstract: We present a Galaxy based web server for processing and visualizing deeply sequenced data. The web server’s core functionality consists of a suite of newly developed tools, called deepTools, that enable users with little bioinformatic background to explore the results of their sequencing experiments in a standardized setting. Users can upload pre-processed files with continuous data in standard formats and generate heatmaps and summary plots in a straightforward, yet highly customizable manner. In addition, we offer several tools for the analysis of files containing aligned reads and enable efficient and reproducible generation of normalized coverage files. As a modular and open-source platform, deepTools can easily be expanded and customized to future demands and developments. The deepTools webserver is freely available at http://deeptools.ie-freiburg.mpg. de and is accompanied by extensive documentation and tutorials aimed at conveying the principles of deep-sequencing data analysis. The web server can be used without registration. deepTools can be installed locally either stand-alone or as part of Galaxy.

1,376 citations


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Performance
Metrics
No. of papers in the topic in previous years
YearPapers
20225
2021416
2020874
20191,569
20181,569
20171,598