1. Matthew Matlock
  2. Eratosthenes

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Eratosthenes

Table of Contents

Introduction

Headache-free, BibTeX-based management your academic reference library.

Check out the tutorials below and be sure to read about using Eratosthenes with BibDesk or JabRef if you plan to do that.

Latest Changes

Please see the Change Log

Features

  • Dropbox Integration (Sync library and attachments)
  • Google Drive Integration (Sync library and attachments)
  • JabRef format bib file support
  • BibDesk format bib file support
  • Supports import from multiple external services
    • .bib files and .zip archives
    • Google Scholar (incl PDFs)
    • PubMed (incl PDFs from PubMedCentral)
    • PubMedCentral
    • DOI
    • ISBN
    • PLoS CompBio
    • Science Magazine
    • Nature Journal
    • Wiley Online
    • NEJM
    • American Chemical Society
    • Oxford Journals Bioinformatics
    • Science Direct
    • Journal of Biological Chemistry
  • Reference export
    • Export BibTeX citations and attachments to e-mail, or other sharing services (Recipients using Eratosthenes can automatically import bibtex and attached files from their e-mail app)
    • Export LaTeX citation commands
    • Export plain text formatted citations (ACS style currently supported)
    • Export entries to new bibtex file
  • Productivity features:
    • Attach files and external links to entries
    • Full featured BibTeX editing capability
    • Search google scholar from an entry (help find a pdf for example)
    • Integrated into the android environment, recognizes browser urls for services, recognizes .bib files
    • Recognizes PDFs from the web, allowing direct attachment to an entry from the browser
    • Parse additional metadata from links to supported resources (ie PubMed)
    • Annotate entries to include your own notes, summary information, and keywords
    • Quick search for most BibTeX fields, click on author names, journal, year or other fields to find matching papers.
    • Automatically convert between UTF-8 and LaTeX character codes
  • Multiple Library organizational systems
    • Search fields: author, title, keywords, journal, year, etc
    • Mark Entries Read/Unread
    • Add Favorites
    • Groups/Folders (Maps to BibDesk static groups and JabRef top-level groups)
    • Collections (Higher level organization tool)
    • Keywords
    • Sort entries by date, collection, title, or author
    • Add custom sort field definitions

Planned Features

  • Extended support for JabRef filter groups/search groups and BibDesk smart groups (rudimentary support for JabRef search groups is available)
  • Support for complex search queries
  • Full support for the JabRef Groups Tree nesting structure
  • Graph-based citation explorer (with local library, PubMed and Scholar integration)
  • Syntax highlighting for raw BibTeX editor

Tutorials

Editing Entries

Most of the editing tools in eratosthenes allow for two editing modes. Clicking the 'edit' icon, or clicking on a field in an entry or clicking on a string in the string editor will open up a wizard style entry editor where you can make changes. Long pressing on the 'edit' icon, long pressing on a field in an entry or long pressing on a string in the string editor will allow you to edit the raw BibTeX code for that entry or string.

Using Eratosthenes with Dropbox

Using Eratosthenes with Dropbox is simple.

First, I suggest you open the 'settings' menu and check 'Keep Remote', this will keep your PDFs stored remotely in dropbox, and only fetch the ones you actually access. There are caching options to tell Eratosthenes how many PDFs to keep locally. If you want to download ALL of your PDFs to your device, leave this option unchecked.

Next, choose the 'Database' menu (small file icon) and choose 'Open'. Then select the 'Dropbox' tab from the dialog. Next, navigate to and select your .bib file and then press 'Choose'.

Importing very large libraries for the first time may take a little while, depending on whether you chose 'Keep Remote', how many PDFs you have, and how many entries are in your .bib file.

When you make changes to your .bib file, you will need to choose 'Save' from the 'Database' menu (small file icon). After the app successfully saves your .bib, you will need to choose 'Sync' from the dropbox menu (small dropbox icon) to make the changes available to your other devices.

If you'd like to automatically save your files, you can use 'Automatic Saving'. You will still need to 'Sync' your files to dropbox after you make changes.

Operations on groups of entries

Tutorial coming soon.

Using the Search and Attach Workflow

Tutorial coming soon.

Integration with Online Journals and Resources

Using Eratosthenes with Google Scholar

To use Eratosthenes with Google Scholar, you will need to enable "show links to import citations into 'BibTeX'" in the Google Scholar settings (http://scholar.google.com/scholar_settings), accessible through your browser.

When performing searches in Google Scholar, 'Import into BibTeX' should appear below each entry in your search results (you may have to click 'More' or 'Cite'). Clicking 'Import into BibTeX' will allow you to launch Eratosthenes to import the entry, and the attached PDF will automatically be downloaded if it is available.

CHANGED IN v0.7.8: After choosing "Import into BibTeX" from your browser, Eratosthenes will open a new web view where you may have to enter a captcha. Once you enter the captcha and continue (or if your entry is already shown in the web view), you can press "extract" to extract the scholar .bib and .pdf to your BibTeX library.

Please see 'Notes on Browser Integration' below for browser specific differences in functionality.

Using Eratosthenes with PubMed

There are two ways to use PubMed with Eratosthenes.

First, within Eratosthenes, you can add an entry using a PubMed ID by clicking the "+" icon (new entry) in the action bar and choosing "PubMed". This will open a dialog to enter your pubmed ID.

Secondly, Eratosthenes integrates with the android eco system to detect when you are using PubMed in your browser. When you visit a link such as http://www.ncbi.nlm.nih.gov/pubmed/24289228 the android system should allow you to launch Eratosthenes to import the pubmed entry. This integrates nicely with the pubmed search engine, as clicking on entries will allow you to import them.

Please see 'Notes on Browser Integration' below for browser specific differences in functionality.

Notes on Browser Integration

The browser integration has only been tested with Chrome and Firefox. Please note that Firefox will show an 'android' icon on the Address bar whenever you visit a link like the one above. You have to click this android icon to launch Eratosthenes. Chrome should ask you if you want to launch Eratosthenes automatically when visiting such links.

Using Eratosthenes with other journals

Many journals are supported by the current version of eratosthenes. The functionality is similar to the PubMed functionality. Navigating to an article in a supported journal in your browser will prompt to add the article to your .bib library (see notes on firefox browser integration). Articles can also be imported by DOI. This works for all DOIs. For supported journals, this will also fetch the PDF and abstract.

Supported journals and web sources:

  • Oxford Journals
  • ACM Digital Library
  • American Chemical Society
  • Nature
  • Science
  • PLOS
  • New England Journal of Medicine
  • Journal of Biological Chemistry
  • Genome Research
  • Springer Science
  • Wiley Science
  • Science Direct
  • ArXiV
  • PubMed
  • PubMedCentral
  • Google Scholar

Tutorial coming soon.

Using Eratosthenes with BibDesk

Open your BibDesk format .bib file through the "Open Database" menu option, after you choose the .bib file, the "File Settings" dialog should appear. Choose File Type: BibDesk BibTeX.

What works

  • BibDesk Static Groups appear as 'groups' in eratosthenes
  • BibDesk File attachments can be viewed
  • BibDesk Url attachments can be accessed on the EntryDetail page
  • BibDesk keywords

What doesn't

  • BibDesk Smart Groups are not yet supported
  • Bdsk-file-x style file attachments cannot be added or removed within Eratosthenes, due to the apple file-system specific features of BibDesk, however, a workaround is available to add files to your bibdesk entries (see Using Eratosthenes File Attachments with BibDesk)

Using Eratosthenes File Attachments with BibDesk

When adding new file attachments to a BibDesk file from Eratosthenes, Eratosthenes will export these files as local-url fields in bibtex. Each local-url field contains a relative path to the attached file.

If more than one local-url is present, the subsequent fields will be numbered ie: local-url, local-url-2, local-url-3, etc.

For a single attachment (just a local-url field, no local-url-x) you can convert these to bdsk-file fields in BibDesk by using the "Database->convert file and url fields" menu option.

For multiple attachments, you will have to add each local-url-x field using the "Preferences->Default Fields" menu in BibDesk.

Using Eratosthenes with JabRef

Open your JabRef format .bib file through the "Open Database" menu option, after you choose the .bib file, the "File Settings" dialog should appear. Choose File Type: JabRef BibTeX.

What works

  • JabRef top-level groups
  • JabRef file attachments can be viewed, added, and removed
  • JabRef url attachments can be viewed on the EntryDetail page
  • JabRef keywords
  • Simple JabRef search groups such as basic search queries and field=value queries are supported (v0.7.12)

What doesn't

  • Subgroups in the JabRef group-tree. Only the root level groups will appear in Eratosthenes
  • Complex JabRef search groups are not supported, e.g. REGEX is not supported, and/or is not supported, etc.
  • JabRef entry markup (color highlighting) is not yet supported

Switching to Eratosthenes from a desktop solution

If you are interested in ditching your desktop solution all together, and going with Eratosthenes, I highly recommend converting your .bib library to the Eratosthenes native format. To do this, open your library using either Jabref or BibDesk mode. Then, switch compatibility mode to "Eratosthenes" and save your library from the database menu.

WARNING: This is typically a one-way operation so please make a backup. In particular, it is impossible to re-save an Eratosthenes formatted .bib file as a BibDesk database due to BibDesk's use of proprietary apple file reference schemes.

Legal Notice

External Software Libraries included in Eratosthenes

PinnedHeaderListView: https://github.com/JimiSmith/PinnedHeaderListView Copyright (c) 2012, James Smith All rights reserved.

JBibTeX: https://code.google.com/p/java-bibtex/ Copyright (c) 2012 University of Tartu All rights reserved.

Privacy Policy

Eratosthenes does not collect or transfer any user data from your device without explicit action on the user's part. Data concerning the current state of the application can be e-mailed to the developer using the application's "Report" feature, which is available to the user when an error occurs. This information is used ONLY for the purposes of debugging reported problems. This data is never published in the public domain in any form and is never used to obtain personal or otherwise sensitive information about the user.

License

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL Matthew Matlock BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

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