sennoma's Bookmarks About (openscience) AND "webtools"

Science Pipes

SciencePipes is an environment in which students, educators, citizens, resource managers, and scientists can create and share analyses and visualizations of biodiversity data. It is built to support inquiry-based learning, allowing analysis results and visualizations to be dynamically incorporated into web sites (e.g. blogs) for dissemination and consumption beyond SciencePipes.org itself. For more information: * further introduction * presentations * status of the site * NSDL article about SciencePipes.org Alpha functionality demos: * uploading and running a Kepler workflow * editing a pipe in the SciencePipes.org authoring environment SciencePipes is a project of the Cornell Lab of Ornithology Information Science Program and is funded by the National Science Digital Library.

by sennoma 2009-10-06 01:05 scholarlycommunication · openscience · webtools

http://sciencepipes.org/alpha/home - cached - mail it - history

Main Page - BioDAS

by sennoma 2009-01-25 15:49 webtools · openscience · opendata

http://www.biodas.org/wiki/Main_Page - cached - mail it - history

biological wiki comparison

http://friendfeed.com/e/4ad4515b-fd30-4f9f-bf5c-6a1381692fdc/Comparison-of-biological-wikis/

by sennoma 2009-01-24 00:29 wiki · openscience · opendata · webtools

http://spreadsheets.google.com/ccc?key=pEEe7xKalAhYdf56DWRfcQg - cached - mail it - history

PLoS Computational Biology: Defrosting the Digital Library: Bibliographic Tools for the Next Generation Web

by sennoma 2008-11-01 01:22 webtools · openscience

http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000204 - cached - mail it - history

» Workshop: Web 2.0 for Scientists / Cool Tools for Scholars Computer Science & Engineering Resources: Reseach Resources for CSE and Other Students at York University, Toronto

by sennoma 2008-10-21 12:57 openscience · tools · webtools · web2.0

http://www.yorku.ca/yul/cse/?p=59 - cached - mail it - history

Nascent: EUtils, Pipes, Ubiquity, preprints and semi-automatic categorisation

by sennoma 2008-09-18 20:31 openscience · oa · webtools

http://blogs.nature.com/wp/nascent/2008/09/a_bundle_of_web_tools.html - cached - mail it - history

The OpenScience Project » Exhibit: make your data web-accessible

by sennoma 2008-09-18 12:16 webtools · openscience

http://www.openscience.org/blog/?p=245 - cached - mail it - history

Opening science: How unconferences changed my life « Ouroboros

by sennoma 2008-08-14 16:54 openscience · webtools

http://ouroboros.wordpress.com/2008/08/14/opening-science-how-unconferences-changed-my-life/ - cached - mail it - history

Science in the open » Facebooks for scientists - they’re breeding like rabbits!

by sennoma 2008-08-01 14:50 lostart · openscience · webtools

http://blog.openwetware.org/scienceintheopen/2008/08/01/facebooks-for-scientists-theyre-breeding-like-rabbits/ - cached - mail it - history

myExperiment

by sennoma 2008-05-17 21:30 webtools · openscience · ELN · social.science · socialsoftware · workflow

http://www.myexperiment.org/ - cached - mail it - history

One Big Lab: New paper-protocol-lab-knowledge sharing website out of Stanford

by sennoma 2008-04-12 01:21 webtools · collaboration · social.science · openscience

http://onebiglab.blogspot.com/2008/04/new-paper-protocol-lab-knowledge.html - cached - mail it - history

HubLog: Generate a bookmarklet to automate offprint requests

Last week, Pierre Lindenbaum made the bold move of creating a bookmarklet that would find the author's email in the HTML version of a paper and automatically create an email asking for an offprint (authors are generally happy to send copies of their own papers - at least they don't have to pay the postage any more).

by sennoma 2008-01-15 19:52 webtools · science · openscience · oa

http://hublog.hubmed.org/archives/001385.html - cached - mail it - history

Nucl. Acids Res. -- Table of Contents (January 2008, 36 [Database issue])

by sennoma 2008-01-14 04:59 oa · opendata · webtools · openscience

http://nar.oxfordjournals.org/content/vol36/suppl_1/index.dtl?etoc - cached - mail it - history

Main Page - YourSciComWiki

by sennoma 2007-12-08 12:35 openscience · webtools

http://www.yourscicom.com/w/index.php?title=Main_Page - cached - mail it - history

prometeonetwork

A free, online, global network of Doctors and Researchers in Life Sciences Mission: To provide researchers in Life Sciences and Physicians with a scientific community online, where they can be able to interact with each other. Prometeo Network is a trusted network of connections where information and resources are attainable to every Member.

by sennoma 2007-09-23 22:29 openscience · webtools · collaboration · networking

http://www.prometeonetwork.com/ - cached - mail it - history

openacademia::doc

openacademia.org is an open source publication metadata repository for scientific communities. Our goal is to allow scientists to collect, organize and disseminate publications more efficiently using a combination of novel semantic technologies. openacademia operates on an open source, open data, open documentation principle. Unlike metadata stores maintained by publishers, openacademia gives complete access to your data in the form of RSS, RDF and APIs. Unlike Citeseer or DBLP, openacademia is software you can install and run locally and use it to connect to any other data source around the world. For the technologically minded, our system relies on the idea of dynamically converting BibTex files - a standard for publication metadata - into news channels, following the same format that is used to syndicate and push news items to readers across the Web (RSS). The name for this new standard is BuRST, Bibliographies Using RSS Technology.

by sennoma 2007-09-11 11:00 openscience · webtools

http://www.openacademia.org/doc/index.html - cached - mail it - history

hGene - bioformats.org

Microformats add value to the data you explore and publish on the web. On this site you can find advice, markup and a blog to start using microformats in biology. hGene A working draft for a gene microformat The hGene microformat allows you to add additional semantic information to web pages containing gene data. This allows visitors to use that data in a more flexible way.

by sennoma 2007-08-29 13:43 webtools · openscience

http://www.bioformats.org/hGene/ - cached - mail it - history

ticTOCs - Tables of Contents Service | Project Homepage

by sennoma 2007-08-18 15:17 openscience · webtools

http://www.tictocs.ac.uk/ - cached - mail it - history

News from ticTOCs

by sennoma 2007-08-18 15:17 openscience · blogs · webtools

http://tictocsnews.wordpress.com/ - cached - mail it - history

KForge Demo - Home

KForge Demo is a digital open knowledge community based around this site. It is built on the KForge system and aims to provide you with the facilities and tools to create everything from a new textbook to maps. The only requirement to host a project on this site is that it be open. Tools provided to assist you in your project include: * Wikis, Message forums and mailing lists to help you collaborate. * Content management systems and other publication mechanisms. * Storage facilities and webspace including versioning systems and databases. * A project framework with mechanisms to control access and structure work.

by sennoma 2007-08-16 11:39 openscience · webtools

http://demo.kforgeproject.com/ - cached - mail it - history

Knowble.net - Networking Professors, Researchers, and Scientists

by sennoma 2007-08-15 17:39 openscience · webtools · socialsoftware · collaboration

http://www.knowble.net/login/ - cached - mail it - history

About Scirate.Com

Scirate.com is a new experimental website for trying to deal with the information torrent hoisted upon the typical scientist who attempts to keep up with the latest and greatest in his or her research field. The basic idea is for the site to work as a sort of filter for the daily listings of new papers appearing on the internet. In particular, the site is currently set up to work most closely with the arxiv.org a preprint depository which has daily postings of new papers. By adopting the model of such websites as digg.com users can vote for a paper. These votes then influence which papers are displayed in a given listing. As a larger and larger userbase grows, it is hoped that the effect of this voting will allow users to confidently be directed to the most important papers published in each listing. Of course there must always be a group of people who are considering each paper, so the real hope is that the amortized work involved will improve under such a voting system.

by sennoma 2007-06-21 20:52 openscience · webtools

http://scirate.com/about.php - cached - mail it - history

myExperiment - find, build and share scientific workflows

myExperiment makes it really easy for the next generation of scientists to contribute to a pool of scientific workflows, build communities and form relationships. myExperiment enables scientists to share, re-use and repurpose workflows and reduce time-to-experiment, share expertise and avoid reinvention.

by sennoma 2007-06-13 09:07 webtools · openscience

http://myexperiment.org/ - cached - mail it - history

SciLink.com - Connecting Science Professionals

by sennoma 2007-03-20 13:08 openscience · webtools · bibliometrics

http://www.scilink.com/m2/start.action;jsessionid=1DD9D47B094E1945C58359C687A1EFD7 - cached - mail it - history

Organization Homepage

by sennoma 2007-03-08 22:08 webtools · openscience · opendata

http://www.data360.org/ - cached - mail it - history

Academic Productivity » Online reference management (part 2): going social

In a previous post I presented some considerations on the impact of online reference management (ORM) tools on one’s productivity. Graph of a Connotea user's items from HubLogI haven’t mentioned yet another major advantage of using social software for managing references: the possibility of using dynamically generated feeds to track things you are interested in.

by sennoma 2007-02-24 23:27 webtools · work · openscience

http://www.academicproductivity.com/blog/2006/online-reference-management-part-2-going-social/ - cached - mail it - history

Element List - Science Links for Scientists

List of OA journals, includes some things that aren't exactly journals.

by sennoma 2007-01-31 01:40 openscience · oa · webtools

http://www.elementlist.com/lnx/index.php?action=displaycat&catid=90 - cached - mail it - history

Copyright 2.0 and Open Science

Numly assigns a unique identifier (which can be readily converted to a URL) to any digital object. May be v. useful as blogs become more important sources of original science.

by sennoma 2007-01-06 21:41 webtools · openscience

http://depth-first.com/articles/2007/01/04/copyright-2-0-and-open-science - cached - mail it - history

NAR Database Issue 2007 | nodalpoint.org

by sennoma 2007-01-06 00:17 openscience · science · opendata · webtools

http://www.nodalpoint.org/2007/01/05/nar_database_issue_2007 - cached - mail it - history

Drexel CoAS E-Learning: Google Co-op for Organic Chemistry

Google Co-op: defined search spaces

by sennoma 2006-12-03 22:27 openscience · webtools

http://drexel-coas-elearning.blogspot.com/2006/12/google-co-op-for-organic-chemistry.html - cached - mail it - history

Reactome

The Reactome project is a collaboration among Cold Spring Harbor Laboratory, The European Bioinformatics Institute, and The Gene Ontology Consortium to develop a curated resource of core pathways and reactions in human biology. The information in this database is authored by biological researchers with expertise in their fields, maintained by the Reactome editorial staff, and cross-referenced with the sequence databases at NCBI, Ensembl and UniProt, the UCSC Genome Browser, HapMap, KEGG (Gene and Compound ), ChEBI, PubMed and GO. In addition to curated human events, inferred orthologous events in 22 non-human species including mouse, rat, chicken, zebra fish, worm, fly, yeast, two plants and E.coli are also available. Reactome is a free on-line resource, and Reactome software is open-source. However, please take note of our disclaimer.

by sennoma 2006-11-19 18:20 openscience · webtools

http://www.reactome.org/ - cached - mail it - history

Thinkature

by sennoma 2006-11-09 15:56 webtools · openscience

http://thinkature.com/ - cached - mail it - history

microformats | About microformats

Designed for humans first and machines second, microformats are a set of simple, open data formats built upon existing and widely adopted standards.

by sennoma 2006-09-07 21:53 webtools · reference · oa · openscience

http://microformats.org/about/ - cached - mail it - history

Nucl. Acids Res. -- Table of Contents (34 [Web Server issue])

NAR's yearly compendium of Web stuff. *drool*

by sennoma 2006-07-17 11:00 openscience · oa · webtools · reference

http://nar.oxfordjournals.org/content/vol34/suppl_2/ - cached - mail it - history

ebounce.info

"ebounce.info is a website offering free online tools for purposes related to gathering, sorting, presenting and digesting of information. " New, beta, but worth remembering.

by sennoma 2006-06-26 21:15 webtools · science · openscience

http://ebounce.info/ - cached - mail it - history

Main Page - OpenWetWare

Must see if Peter wants a lab page here.

by sennoma 2006-06-08 17:06 openscience · webtools · work

http://openwetware.org/wiki/Main_Page - cached - mail it - history

Public Knowledge Project

"The Public Knowledge Project is a federally funded research initiative located at the University of British Columbia and Simon Fraser University on the west coast of Canada. It seeks to improve the scholarly and public quality of academic research through innovative online environments."

by sennoma 2006-05-12 12:17 openscience · reference · webtools

http://www.pkp.ubc.ca/ - cached - mail it - history

HubLog: Peer Review with Marginalia

This is in its early stages, but it's way cool -- a way to annotate online documents. Think peer review as wiki; wonder if Biology Direct would be interested?

by sennoma 2006-03-26 13:21 webtools · lostart · openscience

http://hublog.hubmed.org/archives/001339.html - cached - mail it - history