观点|世上最强大的科研工具手册（下）——日常工作管理、论文写作出版和影响力评估

本文转载自网络，经过简单整理和标注。
笔者自己亲测过的靠谱工具已用斜体加粗标注。同时加入了一些适合国内环境的工具/网站。
本文不断更新中，希望有能力的朋友可以到这个网页共同完善这个列表。
原网页PDF版本下载，链接：http://pan.baidu.com/s/1bd7Ru2 密码：2s0x

1. At the bench and in the offic日常工作

Here is a collection of tools that help researchers in their everyday tasks. Go to Lab and project management, for tools that help manage stocks and equipments in the lab as well as project management tools for research. You’ll also find a selection of Electronic lab notebooks developed with academic researchers in mind first. Many others are available elsewhere. Outsourcing experiments is increasingly common in academic research, in part thanks to several sites that are making it easier and cheaper. Platforms to Find and share samples help you disseminate and find materials and biological samples. Under Protocol repository, you will find a collection of publicly accessible resource for experimental protocols. Work with code gathers tools designed to make the coder’s life easier and Work with data tools to generate and analyze data sets, including many R-based tools.

Lab and project management

1degreebio – Reagent marketplace.

Antibody Registry – Gives researchers a way to universally identify antibodies used in in the course of their research.

Asana – Keeps your team organized, connected, and focused on results.

Biocompare – Find products, read reviews and hear about the latest technological developments.

ELabInventory – Web-based laboratory inventory management system designed for life science research laboratories

LabCritics – Provides researchers with a trust-able source of lab equipment reviews and comparisons.

LabGuru – Supports day to day activities of a research group, from vision to execution, from knowledge to logistics.

Lab Suit – Inventory Management, orders Management, materials Trade-In, price Comparison.

Life technologies Lab Management Tool – Management tool for lab equipment and services.

Open Science Framework – Gathers a network of research documents, a version control system, and a collaboration software.

Quartzy – A free and easy way to manage your lab.

Quip – Combines chat, documents, spreadsheets, checklist, and more to collaborate on any device.

StrainControl – Lab management tools that allows you to organize strains, plasmids, oligos, antibodies, chemicals and inventorie.

Synapse – Platform to support open, collaborative data analysis for clear, reproducible science

Electronic lab notebook

Docollab – Helps you manage your scientific research, collaborate with your colleagues and publish your findings.

elabftw – Electromic lab notebook made by researchers, for researchers, with usability in mind.

Evernote – A place to collect inspirational ideas, write meaningful words, and move your important projects forward.

Findings App – Lab notebook app that allows to organize your experiments, keep track of results, and manage your protocols.

Hivebench – Hosted numeric laboratory notebook tool to manage protocols, experiments and share them with your team.

Journal Lab – A community of scientists who share open summaries and peer review of published articles. (blog post)

LabArchives – Web-based product to enable researchers to store, organize, and publish their research data.

Labfolder – Simple way to document your research and to organize your protocols and data. (blog post)

LabGuru – Supports day to day activities of a research group, from vision to execution, from knowledge to logistics.

Laboratory Logbook – Document projects running in a lab and manage experimentally obtained data and its metadata.

sciNote – Open source lab notebook with workflows and modular functionalities. (blog post)

Sumatra – Automated electronic lab notebook for computational projects.

Outsourcing experiments

Emerald Cloud Lab – A web-based life sciences lab, developed by scientists for scientists.

ScienceExchange – Marketplace for shared lab instrumentations. (blog post)

TetraScience – Allows you to monitor & manage your experiments from anywhere.

Transcriptic – A remote, on-demand robotic life science research lab with no hardware to buy or software to install.

Find and share samples

Addgene – Plasmid sharing platform

Antibody Registery – Gives researchers a way to universally identify antibodies used in in the course of their research.

Biospecimens – Platform for biospecimen-based research.

Duke human heart – Repository for cardiovascular research scientists, including tissues samples and information.

ELabInventory – Web-based laboratory inventory management system designed for life science research laboratories.

Nanosupply – Platform facilitating sourcing and sharing of advanced materials for research and education.

Sample of Science – Peer-Sharing Platform for Scientific Samples. (blog post)

Protocol repository

SciVee – Science video sharing platform that includes protocols.

Benchfly – Video protocols and video platform for scientists.

Benchling – Life science data management and collaboration platform, where you can create, find, and discuss protocols.

IPOL journal – Research journal of image processing and image analysis with algorithm descriptions and its source code.

MyExperiment – Share workflows and in silico experiments.

OpenWetWare – Share information, know-how, wisdom, and protocols among researchers working in biological fields.

Pegasus – Platform that help workflow-based applications execute.

Protocols – Crowdsourced universal protocol repository. (blog post)

Protocol online – A curator of protocols contributed by researchers arounds the world.

Scientific Protocols – Share scientific protocols using the GitHub platform.

Work with code

Sublime Text：界面简洁美观、功能强大的文本编辑器。

CDE Tool – Deploy and run your Linux programs on other machines without any installation or configuration.

Dexy – Helps your code to speak for itself with beautiful syntax highlighting.

GitLab – A git repository management, code reviews, issue tracking and wiki’s all in one platform.

iPython notebook – Interactive computational environment that allows code execution, text, mathematics, plots, and rich media.

Kepler – Helps create, execute, and share models and analyses across scientific and engineering disciplines.

Mercurial – Control management tool with distributed source, giving each developer a local copy of the development history.

nanoHUB – Centralized platform for computational nanotechnology research, education, and collaboration.

ROpenSci – Packages that allow access to data repositories through the R statistical programming environment.

Sweave – Allows to embed the R code for complete data analyses in latex documents

System in Cloud – Platform, enabling clients to rapidly draw and execute data-flow diagram that run in cloud.

Work with data

MobaXterm：功能完善的SSH终端，用来远程连接服务器，适合有大规模计算需求的同学。

Benchling – Life science data management and collaboration platform.

Galaxy Project – Web-based platform for data intensive biomedical research.

GenePattern – Genomic analysis platform that provides access to hundreds of genomics tools.

GenomeCompiler – Genetic design platform allowing researchers to manipulate and design everything from single genes to entire genomes.

InSIlico DB – Genomics made possible for biologists without programming.

Kaggle – Patform for data prediction competitions.

Kitware – Advanced software solutions and services for data intensive R&D

mloss – Machine learning open source software.

MyExperiment – Share workflows and in silico experiments

nanoHUB – Centralized platform for computational nanotechnology research, education, and collaboration.

Pegasus – Platform that help workflow-based applications execute.

Plotly – Online tool to graph and share data.

ROpenSci – Packages that allow access to data repositories through the R statistical programming environment.

Statcrunch – Provides data analysis via the Web.

Sumatra – Automated electronic lab notebook for computational projects

SURF In context – Navigate through RDF relations in a smooth and understandable way.

Sweave – Allows to embed the R code for complete data analyses in latex documents.

Synapse – Platform to support open, collaborative data analysis for clear, reproducible science.

System in Cloud – Platform, enabling clients to rapidly draw and execute data-flow diagram that run in cloud.

Tableau – Easily and quickly analyze and present data and share insights.

Taverna – A suite of tools used to design and execute scientific workflows.

VisTrails – Scientific workflow and provenance management system that supports data exploration and visualization.

Wakari – Web-based python data analysis.

WebPlotDigitizer – Web based tool to extract data from plots, images, and maps. (blog post)

Wings – Semantic workflow system that assists scientists with the design of computational experiments.

Wolfram Alpha – Web-based tools for scientific calculations.

World Map – Allows users to explore, visualize, edit, collaborate with, and publish geospatial information.

Fundraising/Grantwriting

Grant Forward – Search engine for research grants.

Pivot COS – A database which includes funding opportunities from all disciplines.

2. Write写作

Writing tools are adapting to the needs of researchers. Tools to store and manage references are grouped under Reference managers. And with research being more and more dependent on collaborations across labs and continents, collaborative writing tools, help researchers write their manuscript while keeping close track of the modifications done by others to the text.

Reference managers

Jabref：参考文献管理软件，同时支持Word和Latex，安装插件后可以方便的在Word中插入参考文献。 

ACS ChemWorx – Collaborative reference manager coupled with tools and services for authors.

CitationStyles – Find and edit CSL citation styles.

Citavi – Reference management, knowledge organization, and task planning solution.

CiteUlike – Search, organize, and share scholarly papers.

Colwiz – Create citations and bibliography and set up your research groups on the cloud to share files and references.

EndNote – Software tool for publishing and managing bibliographies, citations and references

F1000 workspace – A workspace for scientists to collect, write and discuss scientific literature.

Mendeley – A unique platform comprising a social network, reference manager, article visualization tools.

Paperpile – No-fuss reference management for the web (Google docs plugin). (blog post)

Papers – Helps you collect and curate the research material that you’re passionate about.

Zotero – Helps you collect, organize, cite, and share your research sources

Collaborative writing tools

石墨文档：文档、表格合作写作平台，小巧、简洁，支持微信直接登录，可以在微信上直接编辑文档。 

ASCII doctor – Text processor & publishing toolchain for converting AsciiDoc to HTML5, DocBook & more.

Atlas – Write, collaborate, design and publish on a single platform.

Authorea – Platform to write scientific, academic, and technical documents in collaboration. (blog post)

Draft – Version control and collaboration to improve your writing.

F1000 workspace – A workspace for scientists to collect, write and discuss scientific literature.

Fidus Writer – Online collaborative editor especially made for academics who need to use citations and/or formulas.

Overleaf – Online collaborative LaTeX editor, with direct submission to several publishers (ex WriteLaTex)

Penflip – Collaborative writing and version control. (blog post)

Poetica – Get clear feedback, wherever you’re writing.

ShareLaTex – Collaborative on-line editor for for Maths or Sciences.

Stackedit – Markdown editor based on PageDown, the Markdown library used by Stack Overflow.

Typewrite – A simple, real-time collaborative writing environment.

Quip – Combines chat, documents, spreadsheets, checklist, and more to collaborate on any device.

3. Publish 出版 

Open Access platforms offer an alternative publishing model, allowing anyone to visualize published work for free. Researchers can also maximize the exposure of their work by placing their manuscripts in Paper repositories. In addition to becoming more open, articles are bound to become more interactive. A set of tools allowing you to bring additional functionalities such as executable code to your articles are grouped under Support to publication. You can also find tools to help your choose from the thousands of journals in activity under Journal reviews and advisors.

Open access platforms

eLife – Open access to the most promising advances in science.

F1000 – Leading biomedical experts helping scientists to discover, discuss and publish research.

GigaScience – Online open-access open-data journal that publishes ‘big-data’ studies from the life and biomedical sciences.

Limn – Free journal that outlines contemporary problems.

PeerJ – Open access pre-print and publishing of life science research with annotation.

Cureus – A free and open access the medical journal and a place for physicians to build a digital CV.

ScienceOpen – Freely accessible research network to share and evaluate scientific information.

The Winnower – Open access online science publishing platform that employs open post-publication peer review.

Paper repositories

ArXiv – E-prints in Physics, Mathematics, Computer Science, Quantitative Biology, Quantitative Finance and Statistics.

biorXiv – The preprint server for Biology.

F1000 – Leading biomedical experts helping scientists to discover, discuss and publish research.

Figshare – Manage your research in the cloud and control who you share it with or make it publicly available and citable.

Peer Evaluation – Open repository for data, papers, media coupled with an open review and discussion platform.

Peerage of Science – Pre-publication peer review and publishing for scientific articles.

PeerJ PrePrints – Pre-print repository for the biological and medical Sciences.

SlideShare – Community for sharing presentations and other professional content.

Zenodo – A home for the long-tail of science, enabling researchers to share and preserve any research outputs.

Support to publication

期刊影像因子查询系统：查询期刊的最新影响因子。

Collage Authoring Environment – Framework for collaborative preparation and publication of so-called executable paper.

Exec&Share – Openly share the code and data that underlie your research publications.

Google Charts – Create live and interactive charts in your browser.

RunMyCode – Openly share the code and data that underlie your research publications. (blog post)

ORCID – Provides a persistent digital identifier that distinguishes you from every other researcher.

Journal reviews and advisors

Cofactor Science Journal Selector – A journal selector from the editing service Cofactor.

Edanz’s journal advisor – Personal guide that recommends the tools and services you need to get published.

Journal Finder – Elsevier’s service that help you find journals that could be best suited for publishing your scientific article.

Journal Guide – Find the best journal for your research. (blog post)

Journal Reviewer – Aggregates information users provide about their experience with academic journals’ review processes.

Journalysis – A service for academic authors run by academic authors for reviewing experiences with academic journals.

RoMEO – Find out publisher copyright and self-archiving policies.

SciRev – Share your experience with the scientific review process and learn from others to decide where to submit your manuscripts. (blog post)

4. Evaluate research 影响力评估 

New tools are changing the way research in evaluated, both in terms of the scientific value of articles and the overall achievements of researchers. Find under Peer-review, a collection of tools that are changing the peer-review system into a more open and productive process by bypassing journals and editors. Altmetrics are a set of new tools that analyze the impact of you work by other means than impact factor and citations counts.

Peer-review

Academic Karma – Peer review and get peer reviewed faster.

F1000 – Leading biomedical experts helping scientists to discover, discuss and publish research.

Hypothes.is – Sentence-level peer-review to provide commentary, references, and insight on top of online content.

Journal Review – Rate, and review published medical journal articles.

Labii – A suite of web apps for researchers, including an online app for finding, commenting, rating research papers. (blog post)

Libre – Participative reviewing platform (beta testing).

Paper Critic – Review platform for research publications (Mendeley plugin).

Peerage of Science – Pre-publication peer review and publishing for scientific articles.

PeerJ – Open access pre-print and publishing of life science research with annotation.

PubPeer – Search for publications and provide feedback and/or start a conversation anonymously.

Publons – Record, showcase, and verify all your peer review activity.

Pubmed Commons – Share opinions and information about scientific publications in PubMed. (blog post)

Rubriq – Provides an independent peer review prior to submission. (blog post)

ScienceOpen – Freely accessible research network to share and evaluate scientific information.

Wiki Journal Club – Open, user-reviewed summaries of the top studies in medical research.

The Winnower – Open access online science publishing platform that employs open post-publication peer review.

Altmetrics

Altmetric – Tracks what people are saying about papers online on behalf of publishers, authors, libraries and institutions.

ImpactStory – Share the full story of your research impact. (blog post)

PLOS Article-Level Metrics – A suite of established metrics that measure the overall performance and reach of research articles.

PlumAnalytics – Research altmetric service tracking more than 20 different types of artifacts.

Profeza – Showcasing the unvalued work behind each article to provide new, more accurate way of evaluating researchers.

Publons – Record, showcase, and verify all your peer review activity.
本文转自简书，作者青铜红瓦
链接：http://www.jianshu.com/p/851100273d7a

本文由材料牛deer编辑整理。