AI |
|
| Plotty | Platform for building, deploying, and hyperscaling artificial inteligence (AI) |
BIOINFORMATICS |
|
| MANET database | A bioinformatics database that maps evolutionary relationships of protein architectures directly onto biological networks. |
| European Bioinformatics Institute | Tools for bioinformatics. Web based Blast Fasta Clustal. |
BIOINFORMATIC TOOLS |
| Bedtools bedtools.readthedocs.io | Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. |
| BioJava biojava.org | The open-source Java framework for bioinformatics. |
| BioPerl bioperl.org | The Bioperl Project is an international association of users & developers of open source Perl tools for bioinformatics, genomics and life science. |
| Biopython biopython.org | Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. |
| ENCODE encodeproject.org | The Encyclopedia of DNA Elements (ENCODE) is a public research project which aims to identify functional elements in the human and mouse genomes. |
| Ensembl ensembl.org | The Ensembl project started in 1999 with the goal to automatically annotate the human genome, integrate this annotation with other available biological data, and make all this publicly available via the web. Since then, many more genomes have been added to Ensembl and the range of available data has expanded to include comparative genomics, variation and regulatory data. |
| FastQC bioinformatics.babraham.ac.uk/projects/fastqc | FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis. |
| Java java.com | Java is a general-purpose computer-programming language that is concurrent, class-based, object-oriented, and specifically designed to have as few implementation dependencies as possible. |
| NCI Database Browser | A WWW browser to the new and enlarged NCI database (250.000 compounds) with all kinds of nifty output features and links to other services for continued processing. |
| OMICtools omictools.com | OmicX is a global benchmark in big biodata analytics. Powered by machine teaching, its unique dynamic analytics ecosystem deciphers and analyses life science data. |
| OWL | OWL is a non-redundant composite of 4 publicly-available primary sources: SWISS-PROT, PIR (1-3), GenBank (translation) and NRL-3D. SWISS-PROT is the highest priority source, all others being compared against it to eliminate identical and trivially-different sequences. The strict redundancy criteria render OWL relatively “small” and hence efficient in similarity searches. |
| Perl perl.org | Perl 5 is a highly capable, feature-rich programming language with over 30 years of development. |
| Python python.org | Python is a programming language that lets you work quickly and integrate systems more effectively. |
| Samtools htslib.org | Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories - Samtools, BCFtools, HTSlib. |
| UCSC Genome Browser genome.ucsc.edu | The UCSC Genome Browser provides a broad collection of vertebrate and model organism assemblies and annotations, along with a large suite of tools for viewing, analyzing and downloading data. |
CODON USAGE |
|
| Codon Usage Database | Codon Usage Database compiled from CUTG. |
DATA PROCESSING AND ANALYSIS SOFTWARE |
| community.tibco.com/products/tibco-statistica | TIBCO Statistica advanced analytics and data science platform helps you to embed analytics everywhere, empower more people and innovate faster. |
| ibm.com/analytics/spss-statistics-software | The IBM SPSS® software platform offers advanced statistical analysis, a vast library of machine-learning algorithms, text analysis, open-source extensibility, integration with big data and seamless deployment into applications. |
| originlab.com | Origin is an industry-leading scientific graphing and data analysis software. |
| products.office.com/en/excel | Microsoft Excel is the industry leading spreadsheet program, a powerful data visualization and analysis tool. |
| systatsoftware.com/products/sigmaplot | SigmaPlot is a software package for scientific graphing and statistical data analysis. |
| systatsoftware.com/products/sigmastat | SigmaStat provides a wide range of powerful yet easy-to-use statistical analyses designed to meet the needs of research scientists and engineers. |
DATA REPOSITORIES |
|
| re3data.org : Registry of Research Data Repositories | re3data.org is a worldwide registry of research data repositories in multiple disciplines. |
DNA BAR CODES |
|
| Barcode of Life Data Systems | Database of DNA barcodes |
DICTIONARY |
|
| Dictionary of Substances & Their Effects (DOSE, 3rd Electronic Edition) | 2005 edition. Comprehensive compilation of peer-reviewed health and environmental data on several thousand chemical substances. Includes biological, ecological and toxicological risks, hazards, and effects data and regulatory limits for the substances. |
CONFERENCE |
|
| Conference proceedings citation index. | "Conference Proceedings Citation Index helps researchers access the published literature from ... conferences, symposia, seminars, colloquia, workshops, and conventions worldwide." |
MATHEMATICS |
|
| MathSciNet | American Mathematical Society. |
MOLECULAR BIOLOGY SOFTWARE |
| DNAMAN lynnon.com | DNAMAN is a one-for-all software package for molecular biology applications. This package can perform restriction analyses, multiple sequence alignment, PCR primer design, protein sequence analysis, and plasmid drawing. |
| DNAStar dnastar.com/software/molecular-biology | DNASTAR’s Molecular Biology Suite is a comprehensive sequence analysis and alignment software for molecular biology research. The suite provides software solutions for DNA, RNA and protein editing and annotation, Sanger sequence assembly, multiple sequence alignment, virtual cloning, primer design and comprehensive sequence analysis. |
| SnapGene snapgene.com | SnapGene offers a fast and easy way to plan, visualize, and document your everyday molecular biology procedures. |
| Vector NTI thermofisher.com/vector-nti-software.html | Vector NTI software is a completely integrated suite of sequence analysis and design tools that help you manage, view, analyze, transform, share, and publish diverse types of molecular biology data, all within one graphically rich analysis environment. |
| Web of science--all databases | Web of Science All Databases indexes (formerly Thomson Reuters Web of Knowledge) indexes core journal articles, conference proceedings, data sets, and other resources in the sciences, social sciences, arts, and humanities. |
MORPHOMETRY |
|
| Cell Profiler | Extract quantitative measurements for multiple images |
| FIJI | An extended version of ImageJ with various plugins |
| ImageJ | A free software for image analysis |
| L-measure | Quantitative morphologic measurement |
| Neurostudio | Trace dendritic arbor of neurons |
| PATENTS | |
| Google patents | Comprehensive list of patents |
| Derwent innovations index | The world's most comprehensive database of international patent information. |
PROTOCOLS |
|
| Protocol Exchange | Open repository for sharing scientific research protocols. These protocols are posted directly on the Protocol Exchange by authors and are made freely available to the scientific community for use and comment. |
| Springer Nature Experiments | Platform connecting researchers with protocols and methods. |
| jove.com | JoVE creates the ultimate solutions for advancing research and science education by making and publishing videos of scientific experiments from the top laboratories around the globe. |
| cshprotocols.cshlp.org | Cold Spring Harbor Protocols is an interdisciplinary journal providing a definitive source of research methods in cell, developmental and molecular biology, genetics, bioinformatics, protein science, computational biology, immunology, neuroscience and imaging. |
| bio-protocol.org/bio101/Default.aspx | Bio-101 is an online database of life science protocols. Its mission is to make life science research more efficient and reproducible by curating and hosting high-quality, experimentally validated, freely accessible protocols. |
| protocol-online.org | Protocol Online is a database of research protocols in a variety of life science fields. It contains protocols contributed by worldwide researchers as well as links to web protocols hosted by worldwide research labs, biotech companies, personal web sites. |
| Cold Spring Harbor protocols | The database is fully searchable by keyword and subject. |
| Current protocols | Current protocols in bioinformatics; Current protocols in cell biology; Current protocols in immunology; Current protocols in molecular biology; Current protocols in neuroscience; Current protocols in protein science. |
| JoVE. General. | "General" section of the Journal of Visualized Experiments (JoVE), which is an online journal publishing visualized (video-based) biological research studies. |
| Nature Methods | Nature Methods is a forum for the publication of novel methods and significant improvements to tried-and-tested basic research techniques in the life sciences. |
| Nature Protocols | Nature Protocols is an online journal of laboratory protocols for bench researchers. |
| Springer Protocols | Provides access to peer-reviewed biological and biomedical research protocols from the Methods in Molecular Biology, Methods in Molecular Medicine, Neuromethods, Methods in Pharmacology and Toxicology, and Methods in Biotechnology series. |
PRIMER DESIGN TOOLS |
| Array Designer premierbiosoft.com/dnamicroarray | Array Designer is a microarray software that enables fast, efficient design of specific oligos for making whole genome arrays, tiling arrays and resequencing arrays. |
| GenScript Pcr Primer Design | Genscript online PCR primer design tool for perfect PCR and sequencing primers design. |
| NCBI - Primer-BLAST ncbi.nlm.nih.gov/tools/primer-blast | NCBI’s Primer-BLAST tool is for designing PCR primers and checking them for specificity. |
| NIH primer design | Design primers. |
| NIH primer design | Primer blast. |
| ODIN primer design | Primer blast. |
| PCR Primer Design Tool - Eurofins Genomics | The PCR prime rdesgin tool analyses the entered DNA sequence and chooses the optimum PCR primer pairs. |
| PrimeBank-MGH-PGA | Primer Bank is a public resource for PCR primers. |
| Primer Design Tool - Modern Software | Transform Your R&D With Benchling's Cutting-Edge Primer Design Tool. |
| Primer Premier premierbiosoft.com/primerdesign | Primer Premier's search algorithm finds optimal PCR, multiplex and SNP genotyping primers with the most accurate melting temperature using the nearest neighbor algorithm. |
| Primer3Plus - Bioinformatics | The regions of interest can be marked using targets. Returns a list of all possible primers the can be designed on the template sequence. |
| PrimerQuest Tool - Primer Design | Design algorithm includes multiple checks to reduce primer-dimer formation. |
| Real Time PCR Primer Sets | Database of validated primer sets for quantitative PCR. |
PUBLISHING |
|
|
Journal Information |
|
| AccessScience | Multimedia encyclopedia and dictionary covering all major scientific disciplines. |
|
Citations, abstracts and some full-text of articles published by the Association for Computing Machinery |
|
| AGRICOLA | Agriculture, animal sciences, horticulture, hydrology (1970-present). |
| Agricultural & Environmental Science Database | Extensive coverage of environmental science and related disciplines, and including scholarly journals, trade and industry journals, magazines, technical reports, conference proceedings, and government publications. |
|
Archival access to all of the Albert Einstein's Complete Papers |
|
|
Contains indexing and abstracts for nearly 800 core English-language, scientific and technical publications back to 1983. |
|
|
The Avery Index to Architectural Periodicals database offers a comprehensive listing of journal articles on architecture and design, including bibliographic descriptions. |
|
|
An index of the web sites included in the 1999-present annual lists issued by the Mars Best of Free Reference Web Sites Committee of the American Library Association |
|
|
Bibliography includes references to scientific and engineering research related to material and operations in a winter battlefield, the nature and impact of cold on facilities and activities, cold-related environmental problems, and the impact of human activity on cold environments. |
|
| Biodiversity Heritage Library | Books, journals, and other materials on biodiversity from a worldwide consortium of natural history, botanical, research, and national libraries. Provides free access to hundreds of thousands of volumes from the 15th to the 21st centuries. |
| Biological & Agricultural Index Plus | 1983-present. Agriculture, animal husbandry, botany, cytology, ecology, entomology, environmental science, fishery sciences, food science, forestry, genetics, horticulture, microbiology, plant pathology, soil science, veterinary medicine, zoology. |
| An index with abstracts to periodicals in biology and the life sciences. | |
| BioMed Central | Open-access biomedical electronic journals. Articles are also immediately available on publication thru PubMed Central. |
|
Free access to high impact journals published in BioMed Central |
|
|
Collection of full-text, peer-reviewed research journals in biological, ecological and environmental sciences. |
|
|
Pre-publication paper collection |
|
| BIOSIS Previews | Comprehensive index to life sciences research literature. Covers journals (5000+), reports, meetings (1500+), reviews, and books in all areas of biology. Weekly email alerts available. |
|
The Book Citation Index is designed to enhance the powerful discovery and analysis capabilities of Web of Knowledge by incorporating comprehensive book citation data. Researchers can search for and identify the most relevant and esteemed literature along with peer-reviewed journals. |
|
| Botanicus (Missouri Botanical Garden Botanicus Collection) | 1480-1950. Historic botanical literature from the Missouri Botanical Garden Library. |
| Cambridge Scientific Abstracts | Databases in several electronic formats as well as the traditional print journal. They are available through eleven different commercial online hosts and five CD-ROM vendors, while our web-based Internet Database Service (IDS) provides access not only to all of our databases but also to those of several other publishing partners. |
|
Archival access to all of the Charles Darwin papers and notes |
|
|
CINAHL provides indexing for close to 3000 journals from the fields of nursing and allied health. |
|
|
Scientific Literature Digital Library hosted by Penn State |
|
| Monographs in areas of molecular, cell, and developmental biology, genetics, evolutionary biology, neuroscience, cancer biology, and molecular pathology. | |
|
An official publications of the Association of College & Research Libraries, a division of the American Library Association |
|
|
"Current Contents Connect is a current awareness database that provides easy Web access to complete tables of contents, abstracts, bibliographic information, and abstracts from the most recently published issues of leading scholarly journals. |
|
|
Contains cumulative bibliographic citations to statistical books and articles in more than 1,000 journals, with coverage generally extending back to 1974, earlier in some instances. |
|
|
Archival access to all of the Charles Darwin letters |
|
|
Indexes research data, including data studies and data sets, and links them to the scientific literature to track data citation. |
|
|
America’s libraries, archives, and museums |
|
|
Free, full text journals, mostly in the sciences |
|
|
DOAJ is a community-curated online directory that indexes and provides access to high quality, open access, peer-reviewed journals. |
|
| Dryad | Repository of data underlying scientific publications in the basic and applied biosciences |
| Encyclopedia of Life Sciences | Provides 3000+ peer-reviewed articles, images, a glossary of terms, news, and some multimedia files on a wide variety of life sciences topics. Released 2001, continuously updated. |
|
Engineering Village 2 provides access to over 5 million abstracts from Compendex, full text research articles, patents, standards and handbooks, seamlessly. |
|
|
Citation, abstracts, and some full text of unpublished and difficult-to-find technical reports from several different U.S. government agencies |
|
|
Free databases |
|
| FSTA Direct | Published by IFIS Publishing, the FSTA. – Food Science and Technology Abstracts. database is the largest and most respected database in its field, covering all aspects of food science, food technology and food-related human nutrition. The entire FSTA. database is now available directly from IFIS Publishing for the first time in a web-searchable form as FSTA Direct.. |
| Gale OneFile: Agriculture | Nearly 200 titles focused on agriculture and its related fields: from practical aspects of farming to cutting edge scientific research in horticulture. |
|
"Garden, Landscape & Horticulture Index (GLHI) is the premier resource for access to articles about plants and gardens. |
|
|
General science full text features bibliographic indexes (coverage starting 1984), full text (starting 1995), plus graps, charts, diagrams, photos, and illustrations. |
|
| GigaDB | Repository of large scale datasets underlying scientific publications in the biological and biomedical research |
|
Handbook of paleoanthropology / Winfried Henke, Ian Tattersall (eds.) |
"Comprehensive handbook that takes a multifaceted and multidisciplinary approach to palaeoanthropology |
|
Provides web access to more than three-million full-text documents from some of the world's most highly cited publications in electrical engineering, computer science and electronics. |
|
|
Summarizes studies relating to all aspects of immune systems in man and animals, in normal functions and disorders. |
|
|
Free access to citations and abstracts to articles from over 20,000 journals in a variety of subject areas |
|
| IntechOpen | IntechOpen offers peer-reviewed books to the academic and scientific community on an open-access platform. |
|
Index of organism’s names |
|
|
JCR is a comprehensive, and unique resource tool for Journal Citation and Article Counts; Impact Factor; Immediacy Index; Cited Half-Life; Citing Half-Life; Source Data Listing, etc. |
|
|
Provides image and full-text online access to back issues of selected scholarly journals in history, economics, political science, demography, mathematics and other fields of the humanities and social sciences. |
|
| MEDLINE (via EBSCOHost) is the U.S. National Library of Medicine® (NLM) premier bibliographic database that contains more than 22 million references to journal articles in life sciences with a concentration on biomedicine. | |
| MEDLINE (via the National Library of Medicine) is the U.S. National Library of Medicine® (NLM) premier bibliographic database that contains more than 22 million references to journal articles in life sciences with a concentration on biomedicine. | |
| Presents an extensive selection of medical dictionaries, encyclopedias, glossaries, directories, and links to news and information regarding health topics and drug information for the general public. | |
|
Download PDFs in education, science, and medicine |
|
| National Science Digital Library | Education and research in science, technology, engineering, mathematics. |
| Nature Journals Online | Online access to the journal Nature and its sister publications in Biotechnology, Cell Biology, Genetics, Immunology, Medicine, Neuroscience, and Structural Biology. 1996-present (varies by title). |
| NCBI (National Center for Biotechnology Information) | Platform for biomedical and genomic databases. |
| NCBI Bookshelf | National Center for Biotechnology Information e-books. |
|
A collection of biomedical books that can be searched directly by concept. National Center for Biotechnology Information. |
|
|
An index to the worldwide technical literature pertaining to marine and brackish water environments. |
|
|
Online, full-text handbooks covering topics in physics. |
|
|
The Public Library of Science provides free access to the full-text of all of their highly rated journals |
|
| PLOS (Public Library of Science) | Provides open-access peer-reviewed scientific and medical journal articles and journals. |
|
Retired on September 1, 2019, the Popline database contained "more than 400,000 records" and "provided students and researchers worldwide with access to journal articles, reports, books, unpublished resources, and full-text documents to users in low- and middle-income countries." |
|
|
Searchable and browsable database of dissertations and theses from around the world. |
|
| PubMed | References and abstracts on life sciences and biomedical topics |
|
PubMed / a service of the National Library of Medicine and the National Institutes of Health |
Provides access to over 16 million citations from MEDLINE and other life science journals for biomedical articles back to the 1950s. Includes links to many sites providing full text articles and other related resources. |
|
Major headlines in all science disciplines |
|
| Science Direct | Science journals database. |
| Science Magazine | Science publishing |
|
Behind-the-scenes look at the scientists, journals, institutions, nations |
|
| Science.gov | A gateway to government science information and research results. Searches over 55 scientific databases and 200 million pages of science information with just one query, and is a portal to over 2100 scientific Websites. [Free] |
|
Over 55 databases and over 2100 selected websites from 13 federal agencies, offering 200 million pages of authoritative U.S. government science information |
|
|
An electronic virtual library of scholarly journals published in Latin America. |
|
| SciFinder | Combined access to Chemical Abstracts CAPlus, Registry, CASREACT, CHEMLIST, CHEMCAT databases, and Medline. |
| SciFindern | Next generation SciFinder interface that includes the latest datasets, search features, and mobile support. |
| Provides indexing, abstracting of and citation linking to journals in biology ,physics, chemistry, geosciences, agriculture, medicine, business, social work, and the social sciences. | |
|
Statistical sources at Cornell University |
|
| Web of Science: Core Collection | Access the world’s leading scholarly literature in the sciences, social sciences, arts, and humanities and examine proceedings of international conferences, symposia, seminars, colloquia, workshops, and conventions. |
|
Worldwide catalog of over 100 million books |
|
| Zoological record |
Bibliographical references from more than 6,000 international journals, review annuals, monographs, meeting proceedings, books and reports, representing research in all major areas of zoology, including: behavior, ecology, evolution, genetics, habitat, nutrition, parasitology, reproduction, taxonomy, zoogeography. |
PUBLISHING TOOLS |
| EndNote endnote.com | EndNote is a reference management software that not only frees you from the tedious work of manually collecting and curating your research materials and formatting bibliographies, but also gives you greater ease and control in coordinating with your colleagues. |
| Mendeley mendeley.com | Mendeley is a free reference manager and academic social network that can help you organize your research, collaborate with others online, and discover the latest research. |
| NoteExpress inoteexpress.com/index.htm | NoteExpress is designed to help you organize research notes and bibliographic references, generate bibliographies automatically, and search and capture bibliographic data from Internet with efficiency and ease. |
SEQUENCE ANALYSIS |
|
| Blocks WWW Server | A service for biological sequence analysis at the Fred Hutchinson Cancer Research Center in Seattle, Washington, USA. |
SEMANTIC SEARCH |
|
| WikiProfessional | A web-based research environment for semantic searching, providing an intuitive tool for analyzing and relating concepts. |
SCIENCE SEARCH TOOLS |
|
| Web of Science: All Databases | Provides cross-search of multiple Web of Science databases. |
| WorldWideScience.org: The Global Science Gateway | WorldWideScience.org searches dozens of open access science databases. |
| Zoological Record | Extensive coverage of the world's zoological and animal science literature, covering research from biochemistry to veterinary medicine. |
| WolframAlpha | Provides scientific information for questions |
SEQUENCE ANALYSIS |
|
| Blocks WWW Server | A service for biological sequence analysis at the Fred Hutchinson Cancer Research Center in Seattle, Washington, USA. |
RECODE |
|
| RECODE | The RECODE database is a compilation of ‘programmed’ translational recoding events taken from the scientific literature and personal communications. The database deals with programmed ribosomal frameshifting, codon redefinition and translational bypass occurring in a variety of organisms. |
| Recorder-2000 – The naturalists database | Recorder-2000 – the main database used by recorders/naturalists/ecologists working to National Biodiversity Network (NBN) standards. |
SOFTWARE |
|
| acdlabs.com/resources/freeware/chemsketch | ACD/ChemSketch Freeware is a drawing package that allows you to draw chemical structures including organics, organometallics, polymers, and Markush structures. It also includes features such as calculation of molecular properties (e.g., molecular weight, density, molar refractivity etc.), 2D and 3D structure cleaning and viewing, functionality for naming structures (fewer than 50 atoms and 3 rings), and prediction of logP. |
| adobe.com/products/illustrator.html | Adobe Illustrator is a vector graphics editor developed and marketed by Adobe Inc. |
| adobe.com/products/photoshop.html | Adobe Photoshop is an imaging and graphic design software developed and published by Adobe Inc. for macOS and Windows. |
| Edraw Max edrawsoft.com | Edraw Max is a 2D business technical diagramming software which helps create flowcharts, organizational charts, mind map, network diagrams, floor plans, workflow diagrams, business charts, and engineering diagrams. |
| Image Pro Plus mediacy.com/imageproplus | Image-Pro Plus image analysis software makes it easy to acquire images, count, measure and classify objects, and automate your work. |
| LYSANDRASOFT | LYSANDRA – a software for creating keys and database on different groups of living organisms. By present day we finished completely creating the first key and catalogue on the beetles of the genus Cryptocephalus (Chrysomelidae, Coleoptera) for the Palearctic Region and here we propose the work on CD to your. On our site you can learn all about this work and if it will interest to you, you can order and acquire this work on CD. |
| Morpheus | Converts microarray or qPCR results to heatmaps |
THERMODYNAMIC |
|
| DiProDB | A database to collect and analyse thermodynamic, structural and other dinucleotide properties |
VIDEO |
| Alexander Street Video | Streaming videos and documentaries. |
|
|
WESTERN BLOTTING |
| Western Blotting | Provides scientific information for Western Blotting |