Databases & Tools

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Accelrys Discovery Studio Visualizer

Software for 3D visualization and analysis of biomolecules.

DS Visualizer is an application for analysis and 3D visualization of macromolecules (proteins, RNA, DNA). Its particular strength lies in the intuitive usage as a structure analysis tool: There is no need for reading documentations, just start viewing and manipulating PDB structures in one of the best designed UIs for 3D representations. Simply expand the tree view on the left of the 3D molecule view to select chains or residues down to the single atoms. The selection can be done in the 3D view as well. Selected objects are always highlighed in both places. It's the perfect tool for also for beginners and useres who rarely work with 3D software for visualization of macromolecules.


Software for generating IUPAC names from the structures of the compounds and vice versa.

ACD/Name generates chemical names of organic, organometallic, inorganic or biochemical compounds according to IUPAC and CAS Index rules using the structure of the molecule as input. It generates names in English, French, German and other european languages as well as InChI and SMILES strings.

ACD/PhysChem und ADME Predictors

Software for the prediction of physicochemical properties and ADME characteristics of chemical compounds.

With the PhysChem and ADME modules of ACD/Percepta you can rapidly predict physicochemical (aqueous solubility, logP, logD, pKa, boiling point, etc.) and ADME (blood brain barrier permeation, passive absorption, P-gp specificity etc.) properties from a chemical structure. You can employ batch modules to screen thousands of compounds and investigate the predictions by using different algorithms. In the spreadsheet view the predicted results can be sorted, filtered and color-coded using custom thresholds to facilitate the analysis.

Adobe Fresco

A drawing app for raster and vector graphics.

Drawings can be sent to Adobe Illustrator or Photoshop on a desktop computer, where work can be continued. An Adobe ID is required. Tutorials and additional information are scattered across various web pages and the app thus requires learning by doing.

Adobe Illustrator

Adobe illustrator is a vector graphics application that allows for clean and simple image creation (in 2D).

Adobe illustrator facilitates the creation of logos, drawings, typography, illustrations and, of course, figures for papers as well as group webpages and other applications. Because illustrator artwork is vector based, it can scale up and down easily for different sized screens and thus is valuable for material published on the web. It is possible to create freehand drawings as well as recolor imported photos (rendering the additional use of Photoshop unnecessary for figures). Furthermore, it is possible to import graphs from other programs, such as excel, and edit the colors, font size, and labels as appropriate for making more visually pleasing figures. When writing a paper, if one of the co-writers wants to match colors from old papers, it is possible to import the old figures, register the color, and then match all future figures for consistency.


Altmetric is a provider of qualitative data on the online perception of research, providing an alternative to established, citation-based metrics.

Altmetric data can be accessed on a publication's website via a bookmarklet. The aggregated data is displayed as a colored donut with a number. The number is a weighed sum of different outlets and prevalence of a color indicates a dominating medium wherein the publication was mentioned. Altmetric uses policy documents, news, blogs, social media, academic networks and other sources. Links to the individual sources are provided upon clicking the donut. With your ETHZ email address you can get acces to browse and analyze the publications in the ETH Research Collection.


Anaconda helps to manage and run different versions of programming languages (Python, R and many more) on the same computer and to create the necessary environment to run older packages with different dependencies.

The free, open-source distribution let's you run different development enviroments (JupyterLab, JupyerNotebook, Qt Console, Spyder, Glueviz, Orange, RStudio and VS Code) with exact control of the language and package version. Ideal for scientific computing (data science, machine learning applications, large-scale data processing, predictive analytics, etc.). Anaconda is very beginner-friendly, but comes at the price of great memory requirement.


antiSMASH is a tool to annotate and analyze biosynthetic gene clusters for the production of secondary metabolites from a given genome sequence.

antiSMASH is a tool that allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal and plant genomes. It does so by combining and cross-linking different tools and databases, which are commonly used for in silico analysis of genome sequences and the analysis of secondary metabolites.

The tool not only identifies gene clusters, but also identifies related, homologous gene clusters in other species and if possible for the given class of secondary metabolite gene cluster also predicts the chemical structure of the compound that is produced.

Autodesk Sketchbook

An app for professional concept sketches and more. Ideal for sketching and drawing. The mobile version is free.

In Autodesk Sketchbook, sketching is at the heart of the creative process. Sketchbook comes with many powerful tools for sketching. Autodesk is market leader for CAD software, particularly for architects. Tutorials and more information are scattered across various web pages and the app thus requires learning by doing.


BASE (Bielefeld Academic Search Engine) is a search engine for scientific texts.

It indexes and searches not only journals, but also many university repositories and thus works such as dissertations.

Bealls Liste (a backup)

Beall's List, a creation of Jeffrey Beall, includes criteria for categorizing predatory journals and lists publishers that meet those criteria.

The original list was removed by its creator, however, a copy remains accessible.

Predatory publishers provide limited publishing services while pretending a much higher standard and reputation than they actually have. When publishing in a journal for the first time, ask yourself:

  • Is the journal or publisher listed in Beall’s List?
  • If claiming to be an open access journal, is the journal in the DOAJ?
  • Is the publisher a member of recognized professional organizations?
  • Is the journal truly indexed?
  • Is the journal transparent and following best practices in editorial and peer review processes, governance, ownership and COPE guidelines?

Information on why Beall's original list disappeared can be found in the web or here.


Bioconductor is a free, open source and open development software project and focuses primarily on R. The project distributes various packages for specific R applications and genome annotation packages for microarrays.

Bioconductor offers add-on modules as R packages in order to enable the R user to analyze all types of genomic data, including Affymetrix microarrays, SAGE, nucleotide sequences, and SNP data. It is updated twice per year following the released R updates and provides bugfixes and new packages. In addition to R, Bioconductor also contributes to other programming languages.


Your digital journal stack: App for managing, browsing and reading freshly published articles and journals.

Browzine is a digital bookshelf, in which one can organise, download and read journals avaialbe via ETH library. New articles and issues are automatically flagged, so one does not lose track. Articles can be saved and read offline at a later point in time.

CAS Source Index (CASSI) Search Tool

The CAS Source Index (CASSI) Search Tool is an online resource for retrieving accurate bibliographic information like journal abbreviations and their full titles.

This free resource can be used to quickly and easily look up or confirm past and present publication titles and abbreviations, as well as CODEN, ISBN, or ISSN codes. The CASSI database contains a listing of publications indexed by Chemical Abstracts Service (CAS) since 1907.


Program for drawing chemical structures and reaction schemes. The web version is called ChemDraw JS.

ChemDraw is a drawing tool for chemists and biologists to create molecules and reactions for use in laboratory reports, studies and publications and for querying chemical databases, now including SciFinder, Reaxys or Google. ChemDraw features biopolymer tools, and conversion from and to various chemical strings such as SMILES and InChI. You can draw and view structures in 2D, or render in 3D. To download please register with your top-level domain e-mail:

Chemical Translation Service

A web application for interconverting chemical identifiers.

A user friendly online application for conversion of chemical identifiers, including CAS, CHEBI, compound formulas, Human Metabolome Database HMDB, InChI, InChIKey, IUPAC name, KEGG, LipidMaps, PubChem CID+SID, SMILES and chemical synonym names. Batch convert services are supported, submitting multiple chemical identifiers of the same type and yielding a table of converted identifiers. The results can be viewed directly and/or downloaded in different formats including CSV, XLS, PDF and XML. The tool can also be queried directly using a REST API.

Chemistry by Design

Flashcard app for practicing the thinking skills used for multistep organic synthesis.

The app guides through synthetic sequences in a stepwise manner, depicting starting material, reagents and product for each step as a flashcard. It features a quiz mode wherein reagents and products are hidden under grey boxes. You can do some guesswork before looking at the solution by simply tapping. At the end of each synthesis there is a direct DOI link to the primary literature.

Chemistry Reference Resolver

Copy a citation or a DOI into the field, to get to the chemicle article webiste in one click. Works with up to 10 citations simultaneously.

The Chemistry Reference Resolver takes as input a text reference to a published article in a variety of formats and then finds and displays the corresponding publication by pointing the users to the webpage where the citation is hosted. It can also be used to retrieve patents and safety data sheets or look up a chemical at Aldrich via its CAS number. The search bar add-on is especially fast: Just copy in a reference and get to the article, without having to load the website. Using the Chrome extension, references can be resolved by selecting and right click.

ChemSpider API

ChemSpider data can be accessed via RESTful API.

A set of endpoints that provide search and data retrieval for compounds. 1000 queries per month are free, for more, a subscription is needed. ChemSpiPy is a Python wrapper available through pypi.

ChemSpider InChl Web Services

Tool for converting various textual identifiers for molecular structures (InChI, SMILES, Mol), but also for batch searching the ChemSpider database.

ChemSpider InChI Web Services is an online converter for textual identifiers of molecules. The following list is a selection of the most important conversions:

  • Generate InChI
  • InChIKey to InChI
  • InChIKey to Mol
  • InChI to InChIKey
  • InChI to Mol
  • InChI to SMILES
  • IsValidInChIKey
  • Mol to InChI
  • Mol to InChIKey
  • SMILES to InChI


Citavi is a reference management software package, used to create/manage literature databases and quickly adding references and bibliographies when writing theses and publications. For Windows or as a VM for iOS.

In Citavi you can process your collected pdfs with highlighter and comments, and tagging with keywords can help to retrieve your information at a later point. A remarkable feature is the Knowledger Organizer, which facilitates working with ideas, corresponding text snippets and their references. Supports MS Word and various TeX editors. There is currently no site licence at ETHZ.

Cite Them Right

Cite Them Right advises students on how to reference correctly across eight referencing styles.

What makes Cite Them Right unique is the range of referencing styles which can be accessed, including Chicago, Harvard, APA, IEEE, MLA; as well as teaching the user how to reference just about any source. This platform contains useful articles and videos which help to guide students into common queries around referencing, including how to avoid plagiarism and understanding the differences between secondary and primary sources.


CoGe is an online system for making the retrieval and comparison of genomic information and sequence data quick and easy.

Here is a typical work flow: Start with your favorite genome (mouse), do a whole genome comparison of it to human using SynMap, identify a region with an Inversion, compare the breakpoints of that region in high-detail using GEvo, extract out the human sequence using SeqView, find all the protein coding regions using FeatView, use them to find homologs in other vertebrate genomes (e.g. chimp, mouse, and platypus) using CoGeBlast, validate putative syntenic regions using GEvo and more!


All about words: word of the day, vocabulary portal for over 290 languages.

The international language corpora portal (in English) allows you to look up words in 250 different languages


Offers for search capabilites beyond what is possible by using the web interface. Ideal for large scale projects.


Accessible via Python.


DeepL is an online translation tool that delivers better results than google translate.

DeepL translates texts quickly and precisely, using an unspecified neuronal networks approach. If you click on a word in the translated text, other words and phrases are suggested. More than 20 European languages are supported, including German, English, French, Spanish, Dutch and Polish. There are also Chinese and Japanese.

The Pro version of Deepl can be licensed via the IT-Shop of ETH. This way there is no character limit anymore and you have a higher limit for the number of whole documents that can be translated.


A web tool for quickly drawing schemes and diagrams, e.g. flowcharts.

The vector drawing programme offers functions to draw different shapes, lines, arrows and sequences. There are templates for a wide variety of diagram types, such as organigrams, entity relations, Venn diagrams, room divisions, networks or circuit diagrams. The results can be exported as png, svg, html or xml.

DOAB Directory of Open Access Books

In this directory you can search for books that have been published Open Access and can be used freely.

You can search by keyword and filter by publisher, year or even subject.

DOAJ Directory of Open Access Journals

In this directory, you can search for a journal title and quickly find out if it is an pure open access journal.

There is also information about article processing fees (APCs) and the Creative Commons licenses used.


Doodle is an online polling tool for setting dates/times for events. This helps to reduce unneccesary email traffic. ETH Campus License.

You can create polls e.g. giving a list of possible dates for a meeting and distribute them via link. You can opt to get email updates for every person that has just completed the poll. The currently most popular choices are nicely highlighted in real-time and the final result can be exported as an excel file.

Doodle offers possibilities to connect to Outlook, Google Calendar and iCal. Login via SSO and ETHZ-email. This means that new appointments entered in your calendar are automatically indicated as blocked in the appointment polls.


User-friendly tool for creation of word clouds from documents such as articles or abstracts. Inspired by Jonathan Feinberg's legendary Wordle, which is no longer available.

The cloud gives greater prominence to words that appear more frequently in the source text. You can tweak your clouds with different fonts, layouts, and color schemes. The images you create with Wordle can be printed or saved.

Electronic Journals Library University of Regensburg

Look up even obscure journal titles and abbreviations that you find nowhere else and learn what is their publisher.

The Electronic Journals Library University of Regensburg provides a comprehensive catalogue of journals including publication history and more info. It even lists journals that have long since ceased to exist or are now published under another name.

Elsevier Researcher Academy

This online training resource offers short courses in field-independent skills such as research preparation, writing, publishing, peer-reviewing and science communication.

Learn about a broad variety of topics such as writing grant applications, research data management, manuscript preparation, writing skills, technical or book writing, scientific publishing, ethics, finding the right journal, fundamentals of peer-review, social impact of science and ensuring visibility.


EndNote is a reference management software package, used to create/manage literature databases and quickly adding references and bibliographies when writing theses and publications. Available as web-based, iPhone or desktop version.

In EndNote you can process your collected pdfs with Highlighter and Notes, and tagging with keywords can help to retrieve your information at a later point. Endnote databases, attached files and annotations can be synchronized across many devices. Supports MS Word, OpenOffice and BibTeX (via export). Can connect to databases like PubMed and Web of Science.

Many valuable features are restricted in the free online-only version EndNote basic. EndNote can be licensed via the ETH IT-Shop. ETH library regularly offers hands-on training sessions.


A comprehensive gene set enrichment analysis web server.

Software for analyzing gene sets generated by genome-wide experiments. Enrichr program contains a large collection of diverse gene set libraries available for analysis and download.

It is a comprehensive resource for curated gene sets and a search engine that collects biological knowledge including GO terms, pathways, transcriptional profiles.

If you enter gene sets from your analysis, the Enrichr program interprets it and shows the results about GO terms (biological Process, Cellular Component, Molecular Function), KEGG pathways, Genes associated with NIH grants, Transcription factors and so on. It is free, includes many accumulated genomics, transcriptomics and proteomics data and hase nice visualization of enrichment results.

EPPI Reviewer Web

Online tool for reference management, data analysis and information synthesis. Ideal for all processes involving large numbers of articles as encountered in the literature review process, writing systematic reviews and meta-analyses. Subscription on a monthly basis.

In addition to common tools that are necessary for electronic search, bibliographic management, categorizing, collaborating, screening, coding, data analysis and visual presentation of the outcomes, some advanced features including text mining, term extraction and data clustering are also provided by the software.


A news aggregator that collects updates from your favourite newspaper, websites, blogs, Twitter and RSS feeds without you needing to visit the page. For browser, Android and iOS.

Items and sources can be searched, organized, read or marked as "read later". Connections to other tools like Evernote, OneNote, Trello or Slack are available.

Free DOI Lookup

Retrieve the DOI (Digital Object Identifier) for a given article e.g. by means of title and author name.

CrossRef is an international association of scholarly publishers that develops shared infrastructure to support more effective scholarly communications. The network covers over 60 million journal articles and other content items (books chapters, data, theses, technical reports) from thousands of scholarly and professional publishers around the globe. CrossRef currently provides a number of ways to locate a DOI: If you have bibliographic data for an item and would like to find the DOI, please use "Bibliographic metadata search". If you only have an article title and author, please use the "article title" search section of this form. If you have the text of a bibliographic reference, please use "Simple Text Query".


The world's largest library of book summaries. Expand your knowledge with 5-page summaries that you can read in 10 minutes or less. Main focus is business, but there is a broad selection of other books, too, e.g. auxilliary skills or classics.

Compressed Knowledge: The best of knowledge in concise summaries that include all basic facts and statements of the latest, sharpest and most relevant books. The summaries are mainly available in English and German.


ETH offers free access to this version control software, which is hosted in-house.

Git is currently the most popular version control system for tracking changes and collaborative editing of source code. While Git is primarily used by software developers, it is becoming more and more popular in the scientific community as well. In fact, Git can be used to track changes to any piece of digital information. GitLab is a web-

Google Alerts

With Google Alerts you can subscribe to email updates when a new hit appears for an interesting search.

If one has created a good search query, this is carried out continuously and automatically again and again. So you can easily stay up to date.

Google Books

Google Books allows a full text search of more than 40 millions of books as well as journals/magazines.

The books are either out of copyright or have been scanned in collaboration with major libraries. With a glance, you can see where and how often your search terms appear in the book. If the book is out of copyright, or the publisher has given permission, you'll be able to see a preview of the book, and in some cases the entire text. If it's in the public domain, you are free to download a PDF copy. If you find a book you like, click on the "Buy this book" and "Borrow this book" links to see where you can buy or borrow the print book, like e.g. in the Info Center.

Google Images

Google Images is the most comprehensive search engine for image content on the web.

Very helpful is the filter for usage rights, because with it you can specifically find images that you can use freely. In addition to the keyword search, Google Image has a reversed image search. By clicking on the camera icon, an image or the URL to an image can be uploaded and a search for websites that contain this image can be performed. If this particular image cannot be found, links to similar images are displayed.

Google N-gram viewer

A web service for visualizing the occurence over time of a phrase consisting of n words (n-gram) in Google Books.

You can also specify wildcards in queries, search for inflections, perform case insensitive search, look for particular parts of speech, or add, subtract, and divide ngrams.

Google Patents

Find patents via Google.

Unlike Espacenet, Google Patents provides PDFs of patents that have been OCRed and are searchable. This is very helpful for quickly searching for information in long patents.

Google Scholar

A free search engine for the scholarly literature and case law.

To keep up with current developments, you can create alerts for search terms. Legal proceedings can be found under case law. Search for ETH Zurich under Settings/Library Links and activate ETH Get It to access articles available in print at ETH.

Google Translate

The free online translation service from Google translates text and web pages in seconds and from 103 languages.

When Google Translate generates a translation, it looks for patterns in hundreds of millions of documents to help decide on the best translation for you. By detecting patterns in documents that have already been translated by human translators, Google Translate can make intelligent guesses as to what an appropriate translation should be. These statistical machine translations are not all perfect. The more human-translated documents that Google Translate can analyse in a specific language, the better the translation quality will be. This is why translation accuracy will sometimes vary across languages. Beware that when translating from one non-English language to another, the process in the background will entail two translations steps with English as a stopover.       

Google Trends

Analyze the popularity of google search queries as a function of time.

You can enter your own search terms, look at current hot trends (the top 20), check summaries from past years trends or the past week and look at geographical data associated with the searches.

Henry Stewart Talks

Henry Stewart Talks Ltd is a leading provider of specially prepared, animated, online, audio-visual lectures, seminar-style talks.

HSTalks publishes animated audio visual presentations by world leading experts - advanced content in a user friendly format. ETH Zurich has a subscription to the Biomedical & Life Sciences Collection.

Herdt Books

Herdt offers German manuals for a wide range of software applications.

These are available as german PDFs and are updated regularly to reflect the latest versions of the software. Apart from books on operating systems, office applications, web development and programming languages, there are also a few on auxialliary skills.

Image J

ImageJ is a freely available, Java-based image processing program for scientific image analysis.

ImageJ was developed with an open architecture that can be extended using Java plug-ins and is equipped with a macro recorder. The many plugins make it possible to solve image processing and analysis problems, from three-dimensional live-cell imaging and radiological image processing to data comparison between several imaging systems and automated hematology systems. The plugin architecture and the integrated development environment make ImageJ a popular platform for image processing.


IQVIA is a company specialising in natural language processing and text mining for the biomedical literature. They offer a variety of APIs to perform text processing tasks in this area.

The most valuable functionality is the NLP content store search, which allows one, e.g. in Medline abstracts, to search for complex relations between concepts, for instance what genes are interacting with certain substances, or vice versa. This is not possible in PubMed search.

Content store feature extraction then allows one to further explore, reduce and extract the hits retrieved via content store search.

MedDRA allows extracting terms out of the Medical Dictionary for Regulatory Activities from an submitted text. Another API allows the extraction of healthcare concepts from unstructured text. In addition, there are two APIs to extract biomarkers from and FDA drug labels, respectively.

IUPAC Compendium of Chemical Terminology – The Gold Book

The IUPAC Gold Book is compiled by the International Union of Pure and Applied Chemistry and is the primary source of definitions and standards in chemistry.

The compendium compiles the definitions of terms described in the various IUPAC glossaries and other IUPAC nomenclature documents. It is text and structure searchable and has links between related terms and concepts. In recognition of the contribution of Victor Gold, initiator of the first edition, the compendium is also referred to as the „Gold Book“.

Journal finder (Elsevier)

Find the perfect Journal (from Elsevier portfolio only) for your manuscript.

Enter title and abstract and the almighty algorithm will find the perfect spot for your opus magnum. The list of suggested journals includes typical timeline for refereeing, rejection rate, some impact metrics, open access fees and the expected embargo period.


A free and open-source data analytics, reporting and integration platform.

KNIME can collect different types of data via import or webscraping. These can be processed in various ways and finally visualized or exported. A reusable workflow can be quickly created by drag-and-drop and linking so-called nodes (processing unit). To implement more complex applications, it is possible to integrate Python, R or Wekascripts. For chemical applications there is integration with JChem/Marvin and Schrödinger, which requires buying a separate licence.


Kudos is a Web Service that helps authors to enrich and share their publications with the goal of increasing usage and impact.

Authors can describe their research in plain language, add supplementary information, and then communicate it via social media channels or email. The effect of these actions can be measured via a wide range of metrics.

The Kudos dashboard provides statistics about downloads, citation count, Altmetric score, and many more metrics. It is also an overview of the articles including the additional context and resources that were added by the user.

There is a special registration URL for D-CHAB members. Please contact Dr. Oliver Renn.


Online dictionaries for 9 languages.

Online dictionaries German-English, -French, -Spanish-, -Italian, -Chinese,- Russian, -Portuguese and -Polish, as well as English-Spanish, -French and -Russian including a forum to discuss translations.

LibKey Nomad

LibKey Nomad is a browser plugin that generates direct links to the PDF of papers in various databases and search engines.

Currently, direct links are implemented in Scopus, Web of Science, PubMed, Embase and Wikipedia. Select your own institution when installing, and, if no online access is available, but a print edition is, then you will be taken directly to the corresponding page in Swisscovery.


Dictionary and search in 100 million translations.

Linguee is a unique combination of an editorial dictionary and a search engine. The search results are divided into two parts in Linguee. First, you see clearly structured results from the reliably edited dictionary. This gives you a quick overview of the translation options. Moreover, there are set examples from other sources that give you an impression of how your keyword is translated in context.


With more than 750 millions registered users, LinkedIn is the largest business-oriented social networking service to maintain your contacts, find new business contacts or search for a job.

When you join LinkedIn, you can showcase your work and yourself to get spotted by employers or headhunters, stay in touch with (former) colleagues and business partners, find professionals with certain qualifications, get access to people, jobs, news, updates, and insights based on your network.

Note: Carefully adjust settings to avoid sending or getting unneccessary notifications (spam mail).

LinkedIn Learning

Repository of high quality online courses, e. g. for image processing (Photoshop, Illustrator, etc.), coding, visualizing and more. ETH employees can license LinkedIn Learning via ETH IT-Shop.

LinkedIn Learning offers courses ranging from 1 to more than 10 hours. Available fields are 3D animation, music, business, CAD, design, programming, education, marketing, photography, video and web development. You can further search by keywords, topics, software name and desired career.

LiteMol Viewer

Web tool for the processing/visualization of 3D molecule structures.

Fast web application for 3D visualization of molecules and other related data. It provides standard visualizations of molecules (cartoons, surfaces, ball and stick, etc.), assemblies, symmetry partner, electron density and cryoEM maps. By an integrated PDBe API you can view and explore validation and annotation data. You can directly load molecules into the viewer by just entering the pdb code. Parts of the molecules can be selected by a powerful python-based selection syntax.

Manchester Academic Phrasebank

The freely available database with hundreds of sentence templates that are typically used in academic writing.

The database is based on a corpus of some hundred postgraduate dissertations completed at the University of Manchester and has been further expanded by analysing academic articles from a range of disciplines. As the items in the database are mostly generic in nature using them does not constitute plagiarism. Sentence templates for different sections of academic research articles (Introduction, Results, Discussion, Conclusions) are available as well as templates for various language functions such as expressing criticism, explaing causality, describing trends, etc. The Manchester Academic Phrasebank was created by Dr. John Morley, the director of the university-wide Language Programmes at The University of Manchester.


Annotate a plant genome, visualize high-throughput data in a biological context and compare multiple experiments.

MapMan is a software tool that supports the visualization of data sets in the context of existing knowledge.


Program for drawing chemical structures and reaction schemes. The web version is called Marvin JS.

With MarvinSketch you can create structural drawings for a broad range of chemical compounds and save (SMILES, mol, cdx, InChI) or export (jpg, png, eps) them in different formats. After registering on their website, you can get a free 2 year academic licence.


Mendely is a freely available reference management software package, used to create/manage literature databases and quickly adding references and bibliographies when writing theses and publications. Available as web-based and desktop version.

In Mendely you can process your collected pdfs with highlighter, sticky notes and comments, and tagging with keywords can help to retrieve your information at a later point. Mendely databases, attached files and annotations can be synchronized across many devices and with other people. Supports MS Word, OpenOffice, LibreOffice and BibTeX (via export).

Mendeley also tries to suggest potentially interesting literature based on your library via algorithm.

The Mendeley Institutional Edition which has been licensed by the ETH Bibliothek is a premium version of Mendeley in which the core Mendeley capabilities are enhanced (sharing libraries) and more cloud space is available (100 GB). ETH library regularly offers hands-on training sessions.


Crystal structure visualization, exploration and analysis tool.

It enables you to

  • generate packing diagrams.
  • define and visualise Miller planes.
  • build and explore networks of intermolecular contacts.
  • display space-group symmetry elements.
  • calculate and display voids.
  • generate publication-quality images.

MestReNova (Mnova)

MestReNova is a user-friendly software for the processing, analysis, simulation and presentation of NMR and LC/GC/MS data.

With Mnova you can

  • Handle NMR data from different manufacturers (Agilent, Bruker, JEOL, PicoSpin, Magritek, Nanalysis, Oxford Instruments, and more).
  • Perform analysis of spectra (deconvolution, peak picking, integration, multiplet analysis, etc.).
  • Process your data automatically (1H, 13C, DEPTs or any other 1D NMR as well as any 2D NMR correlations, such as HSQC, HMBC, NOESY, COSY, TOCSY, etc.).
  • Build high quality, publication-ready spectra whilst working up the data.

MNova is available from the ETH IT-Shop.


An alternative to Google that is a bit more respectful of your data privacy.

Metager won't track you and won't create user profiles. You can even open your search results without being tracked by the sites you visit.


Is a highly customizable note-taking, project management and planning software.

You can organise and connect notes, databases, kanban boards, wikis, calendars and reminders. It is also possible to collaborate with other people. Free academic version with your ETH email address.


Obsidian is primarily an app for managing and structuring notes and texts, but also allows other file types.

Text data are stored as easily re-exportable markdown files. For retrieval there's text search, tags, links between notes or a visualization as a network. There is a large community that actively develops extensions. Automation of processes, templates, aggregation of data, the possibilities are endless.

Open Access Button

OAButton is a browser extension that searches for freely available versions of scientific articles to which there is no access through the institution.

The plugin is available for Firefox, Safari and Chrome and after installation it appears as a button in the plugin bar. When you are on the website of the article and click on the icon, it will search for a free version of the article. If none is found, you can also contact the author to ask for a free version.


openBIS is an Open Source Biology Information System, developed and maintained by the Scientific IT Services (SIS) group at ETH.

openBIS can also be used as an electronic laboratory journal in various biological contexts, when chemical structure handling is not required. The openBIS software framework can be easily adapted to the following technologies: High content screening, proteomics, metabolomics and deep sequencing. direct connections to cloud computing are possible.


Open Researcher and Contributor ID (ORCID) assigns researchers a unique identification number (like a doggy tag or social security number).This is important to uniquely identify researchers with common names (e.g. John Smith or Zhāng Wěi) and to distinguish them from individuals of the same name. It also ensures that older publications can be found if a researcher is currently working at a new institution.

ORCID can be used when submitting new manuscripts, so that your ORCID publication list will be automatically updated. You can import earlier publications via Crossref or Scopus and it is possible to create a detailed profile in ORCID.


Advanced scientific graphing and data analysis software.

With over 100 built-in 2D and 3D graph types their point-and-click customization Origin makes it easy to create publication-quality figures. Origin allows the user to automatically update data and parameters, create templates for repetitive tasks, perform batch operations, connect with other programs (MATLAB, LabVIEW, Microsoft Excel) or create custom routines using scripting and C languages, embedded Python, or the R console. Origin also provides various tools for linear, polynomial and nonlinear curve and surface fitting. Additionally it is very helpful in peak analysis, signal processing and spectra fitting. Origin is available from the ETH IT-Shop.


Overleaf is a web service for collaborative work on LaTeX documents. Free of charge via nethz-login.

In Overleaf several authors can work on the same document at the same time and all of them see the latest version. Comments can be added and changes can be tracked. Other valuable functions are the real-time preview and LaTeX error tracking. Integration of Dropbox, Github, Zotero & Mendeley is possible.

Paperpile (with GoogleDocs)

Google's literature management tool is based on Chrome and helps creating/managing literature databaseserences and quick adding of references and bibliographies when writing theses and publications in Google Office. Billed monthly (around EUR 3.-).

In Paperpile you can process your collected pdfs with Highlighter and Notes, and tagging with keywords can help to retrieve your information at a later point. A remarkable feature are summaries, which facilitate working with ideas, corresponding text snippets and their references. Databases, attached files and annotations can be synchronized across many devices.

Phylogeny Analysis is a free, simple to use web service dedicated to reconstructing and analysing phylogenetic relationships between molecular sequences.

Methods that perform well in benchmarking tests are used to build the multiple sequence alignment and tree.

Plan S Journal Checker

The Journal Checker Tool by cOAlition S support you in finding Plan S compliant “routes” through which to publish your articles.

Enter the name of your funder, institution and the journal to which you plan to submit an article, and the tool checks if this combination of funder, institution and journal offers any route to compliance with Plan S.

The current criteria for compliance center on whether a particular journal enables a researcher to publish an article under a CC BY licence without embargo, and retain sufficient copyright to enable compliance with open access policies.


One of our favorites, both for sketching, drawing and painting, preferably with Apple Pencil.

The app Procreate has received the Apple Design award and is an App Store Essential. It ranks among the most powerful drawing and painting apps but is, nevertheless, intuitive to use and optimized for the iPad Pro and the Apple Pencil. The – not free – app is also ideal for artistic illustrations and cover design. The app comes with all kinds of pens, pencils, brushes, canvas, export and import functionalities and many options for customization.

The free handbook with 453 (Artist) respectively 261 pages (Pocket) is not really necessary to use the app – but an excellent service.


PROSS (Protein Repair One-Stop Shop) is a database-based algorithm for the prediction of stabilizing mutations for unstable proteins and is free to academic users.

Starting point of the process is a pdb-file of the protein. Thereof, a multiple sequence alignment is conducted whereby different parameters can be set, e.g. residues crucial for ligand binding or protein-protein interaction considered not being changeable or reducing the multiple sequence alignment to specific taxa. Resulting design suggestions containing different predicted substitutions are subsequently scored in regard of Rosetta scoring functions. For each design fasta and pdb output files are generated. In addition the used multiple sequence alignment and the resulting scoring file are provided for download.


Publons is currently the only place where you can officially disclose your peer review activities.

Publons provides verified peer review and bibliographic information. It details global peer review behavior and provides training resources for early career researchers. Tools are available for publishers to find peer reviewers.


PubPeer enables scientist to search for their publications or their peers publications and provide feedback and/or start a conversation anonymously.

Articles can be searched by DOI, PMID, arXiv ID, keyword or author. PubPeer has also contributed in revealing many cases of scientific misconduct.


Software for 3D visualization and analysis of biomolecules.

PyMOL is an open-source, molecular visualization system working with all data formats in structural biology (PDB etc). PyMOL can produce high-quality 3D images of small molecules and biological macromolecules, such as proteins. Students can obtain a licence freen of charge.


Quarto is an open-source scientific and technical publishing system built on Pandoc

Quarto allows you to combine create Markdown text or Jupyter notebooks with embedded code snippets of Python, Julia, R or Observable with the resulting output, be it numeric or graphic. It can be used to createe reports, presentations, websites, blogs and books. Output in HTML, PDF, MS Word, ePub.


An alternative to Google that is a bit more respectful of your data privacy.

Qwant won't track you and won't create user profiles. There are ads, but no ad cookies and trackers. You can even open your search results without being tracked by the sites you visit.


R is an open-source script-based programming language for which extensive additional packages for various special applications and fields are available.

R offers a variety of options for importing, wrangling, processing and visualizing different types of data. ALL possible types of statistics can be easily executed. RStudio is the recommended standard graphical user interface. Since R is only one letter, using the CRAN acronym helps googling problems with the software.


Learn Named Reactions, understand mechanisms, look at examples from Reaxys and test your knowledge with ReactionFlash for Android and portable Apple devices.

In organic chemistry, reactions – usually named after their discoverers – are a fundamental part of every chemist's toolkit. ReactionFlash helps you learn and understand named reactions: from the famous ones, to those you have forgotten, to those only a Nobel Prize Winner knows! Not only does the app give you the reaction, it also shows you mechanism, published examples from Reaxys, and even allows you to test your skills with the ReactionFlash Quiz. Why spend laborious hours making your own reaction flash cards when ReactionFlash gives you all you need and makes learning fun?

Read Cube Papers (formerly Papers)

ReaCube Papers is a reference management software package, used to create/manage literature databases and quickly adding references and bibliographies when writing theses and publications. Available in an annual subscription model (USD 36) as web-based, mobile or desktop version.

In Papers you can process your collected pdfs with Highlighter and Notes, and tagging with keywords can help to retrieve your information at a later point. Pdfs cannot only be processed in the app, but also in the web application. Papers databases, attached files and annotations can be synchronized across many devices and with other people (up to 30), with unlimited storage space in the cloud. Supports MS Word, OpenOffice, Google Docs, Overleaf, Pages and Manuscript with BibTeX. Can connect to databases such as PubMed/Google Scholar/Dimensions.

Reaxys API

The Chemistry | Biology | Pharmacy Information Centre has licensed access to the Reaxys API, which allows Reaxys data to be obtained in structured form.

Via API you can query and access the following type of data: Structures, reactions, physical and chemical data points as well as literature.


The API can be accessed using Python or KNIME.


An app for managing, browsing and reading freshly published articles and journals. Available in Android, iOS or Huawei app store.

Researcher is a digital periodical shelf where you can organize, access and read journals. New articles or issues are automatically marked so that you don't lose track. Articles can be saved and read offline at a later date. There are interfaces to Mendeley and Zotero.


ResearchGate is the largest academic social networking site and researchers to share papers, ask and answer questions, and find collaborators.

Users can upload research information (papers, data, chapters, negative results, patents, research proposals, methods, presentations, and software code). Users may also follow the activities of other users and engage in discussions with them. There is a function to directly ask for author versions of articles. RG shows also the h-index of a scientist, in addition to the proprietary RG score, which depends on the activity in the network.

Note: Carefully adjust settings to avoid sending or getting unnecessary notifications (spam mail).

Resolve a DOI name

Get to the article with a known DOI.

The International DOI Foundation (IDF) manages the DOI (Digital Object Identifier) system and also provides retrieval tools. Type or paste a DOI number into the text box and click Go. Your browser will take you to the Web page (URL) associated with that DOI.

Retraction Watch

Since 2010, this blog has provided background information on retracted articles.

If you find anything suspicious in a paper you can contact the Reatraction Watch team and they might investigate. There is also a list of papers they are already under scrutiny and a searchable database of retracted articles.


Scholarcy is a webapp that creates summary texts.

These can be own documents or scientific articles via DOI. Summaries with one or two sections can be created at the push of a button, but also flashcards can be created.


scite helps to quickly analyze in which context an article was cited.

One can search by author, DOI or title of an article and scite shows a quick overview whether the article was mentioned positively, neutrally or negatively. One can also quickly consult the corresponding text passages in the citing articles. scite is chargeable and available from USD 12 per month.

Scopus API

ETH Zurich has also licensed the Scopus APIs, which allow Scopus data to be obtained in structured form.

There are distinct search APIs for Scopus, authors and affiliation; there are retrieval APIs for abstract, affiliation and author; there are metadata APIs for citation overviews, PlumX metrics, journal search, journal details and finally there is an API for subject classification. The Python package pybliometrics provides an efficient toolbox for working with the Scopus APIs.


Uploading the submitted or accepted version of a scientific article to a repository is the green way to meet the criteria of Open Access. But how long do you have to wait before you are allowed to do so?

Sherpa Romeo quickly and clearly summarizes which embargo periods apply to which version of the manuscript, as well as which Creative Commons licenses are used. In case of Open Access obligation by the funder, the embargo period may also be shorter than usual.


Startpage is a powerful search engine employing the most advanced metasearch technology without collecting or sharing any personal information. Start using this search enginge to avoid biased retrieval caused by the filter bubble.

You get the results from Google, but without leaving any traces. Neither are IP addresses stored, nor is personal data gathered or passed on to third parties, and no identifying cookies are placed on your browser. Startpage also offers secure SSL encryption, a proxy option that allows anonymous web surfing, full third-party certification, and numerous other privacy features.


Are you looking for statistics to support your claim? The Statista platform provides facts and figures for students and researchers.

Statista provides statistical data on over 80,000 topics from more than 22,500 sources. Industry and company information with key figures on over 1000 companies, trend analyses and forecasts, historical and current facts - the database bundles information for your basic research.

The data sets are prepared according to scientific criteria and for each statistic the available metadata such as source, publication date, number of respondents, etc. are published. Thus, the information is verifiable on Statista and can be used for your research in a scientifically secured way.


STRING provides functional protein association networks from information about physical and functional interactions between proteins.

Data from various sources are aggregated using an easy to use web-based interface. After entering a protein name/sequence, a network of different types of interactions (color-coded) is displayed: experimentally verified, based on the genetic context (neighborhood, fusions, co-occurrence), derived from textmining, due to co-expression or based on protein homology.

The network can be recentered on other proteisn, and further information can be displayed for each individual protein (gene names, protein domains, 3D structures, etc.). Links to further databases are provided (e.g. NCBI, KEGG, UniProt, PDB). There are different viewing functionalities across species like neighborhood (adjacent genes of similar proteins) or fusion (identify fusion proteins). The data can be exported in various formats and an API for developers is available. It is even possible to download the raw data that is used by STRING to generate the network; they are provided under a Creative Commons license.


Edu-ID is an online identity that enables access to services in the whole of Switzerland.

Within ETH, edu-ID allows you to order books or copies of articles via Swisscovery or rent a locker at the information center. Don't forget to link your ID to you ETH-Profile, otherwise there might be fees when ordering books from e.g. Zentralbibliothek Zürich (ZB). Edu-ID can also be used to access Swiss MOOC, Nationallizenzen, some Moodle or OLAT courses or services such as SWITCHdrive.


Free short link service.

There is no data collection and additionally the links are checked for malware.

Tayasui Sketches und Sketches Pro

Among our favorite apps, especially for drawing, illustrating and tracing.

The app Sketches is a sketching app that was developed particularly for mobile devices, featuring a comprehensive set of tools. Sketches is ideal for converting relevant information from photos into a drawing. The free version allows to use more than 4 layers. Sketches is also ideal for artistic techniques, like water color and acrylic painting. Online tutorials can be found on Vimeo.


Synonym and Antonym Finder.

The free online thesaurus for the English language convinces with lexical quality and innovative technology. Not only synonyms and antonyms can be found. The thesaurus inspires and also helps you find the appropriate words

Short link service only for ETH URLs.

To view user numbers, just add a plus sign to the short link.

Unit Conversion

Online unit converter.

A free online conversion tool to easily convert between different units of measurement in more than 70 categories. The Unit Conversion Tool software is also available for download (USD 30.-).


Unpaywall is a browser extension that searches for freely available versions of scientific articles to which there is no access through the institution.

The plugin is available for Firefox and Chrome and after installation a green or gray padlock appears when you visit the web page of a journal article. Clicking on the green version returns the freely available version of the article, whereas gray means that, unfortunately, no free version was found.

VMD-Visual Molecular Dynamics

Software for 3D visualization, animation and analysis of molecules.

VMD is designed for modeling, visualization, and analysis of biological systems but it may also be used to view molecules in general, as it can read various coordinate files to display the contained structure. VMD provides a wide variety of methods for rendering and coloring molecules. Molecular scenes can be saved in various formats or exported to external rendering tools such as POV-Ray, Tachyon and others.


VOSviewer is a free software tool for constructing and visualizing bibliometric networks.

These networks may for instance include journals, researchers, or individual publications, and they can be constructed based on citation, bibliographic coupling, co-citation, or co-authorship relations. VOSviewer also offers text mining functionality that can be used to construct and visualize co-occurrence networks of important terms extracted from a body of scientific literature. Data from Web of Science, Scopus, Dimensions, Lens, PubMed, Crossref, Europe PMC, OpenAlex, Semantic Scholar, OpenCitations, and WikiData are natively supported.


WolframAlpha introduces a fundamentally new way to get knowledge and answers – not by searching the web, but by doing dynamic computations based on a vast collection of built-in data, algorithms, and methods.

WolframAlpha is based on the software Mathematica. The search engine works particularly well for content from exact sciences and is available also as an app. Here you can solve integrals or equations, convert units or calculate various things.


User-friendly tool for creation of word clouds from text.

Words or word groups that occur more frequently in the text are displayed proportionally larger. If certain words are overrepresented, they can also be scaled using the logarithm or square root of the numbers. Clouds can be designed with different fonts, layouts and color schemes. The images can be saved as svg, png or JSON.

Wordpress Blogs

With Wordpress a blog can be created in no time and with little effort. Blogs can be public or restrict access to people with a login.

The blogs can be used for various purposes: As a themed blog for an interested audience, as a forum for the discussion of current literature, as a platform for the exchange of like-minded people, as an archive of read articles, travel or photo diaries, etc... Each ETH member can run up to 5 blogs free of charge.


Zotero is a reference management software package, used to create/manage literature databases and quickly adding references and bibliographies when writing theses and publications. Available as web-based, iPhone or desktop version.

In Zotero you can process your collected pdfs with Highlighter and Notes, and tagging with keywords can help to retrieve your information at a later point. Pdfs cannot only be processed in the app, but also in the web application. Papers databases, attached files and annotations can be synchronized across many devices and with other people. Supports MS Word, OpenOffice, LibreOffice and BibTeX (via export). Can connect to databases like PubMed/Google Scholar/Dimensions/Crossref/arXiv. For ETH members, there's unlimited storage space.