Macs in Chemistry

Insanely Great Science

ChemDoodle 7 released

 

The latest update to the hugely popular chemical drawing package ChemDoodle has just been announced.

Some of the new features in ChemDoodle 7:

  • A new and improved interface based on the feedback from the last 6 years. The new interface is focused on the content and allows you to maximize your drawing areas. Widgets are now floating and can be individually enabled and disabled.
  • ChemDoodle 3D. A new application for creating 3D graphics and more for the sciences. You have full control over the 3D graphics and animations, including text. Distance, angle and torsion measurements are provided. Also a corresponding builder for 3D ChemDoodle Web Components. There is so much more.
  • Full multipage document support. Create lists of pages or grids. Draw between all pages and print them out.
  • BioArt. Large, full color, libraries of new art for use in biological figures, including animals, organs and organelles.
  • A set of 48 safety symbols included in the glassware set.
  • Significant performance improvements, in many cases 20x faster than v6. ChemDoodle will now load faster, work faster and respond faster.
  • New drawing features: collapse fragments to labels, incrementing list attributes (to quickly number or designate parts of structures), new TLC options, rotate atom labels if only a single atom is selected (as opposed to the global option), and more visual specifications among others.
  • Twitter integration.
  • Integration with the LabArchives ELN.
  • Support for both Java 6 and 7 on Mac OS X.
  • Dozens more improvements and additions.

If you want to find out more about ChemDoodle 7 there are a series of Webinars that describe it in detail

I hope to write a review later this week.



Comments

Open Phacts API update

 

The OpenPhacts API has been updated to include two new data sets and the corresponding API calls.

1) DisGeNet target-disease associations These API calls use URIs inputs that correspond to either diseases or targets (proteins or genes). The disease identifiers correspond to UMLS CUIs, Mesh ids or ConceptWiki and can use several namespaces, e.g. http://linkedlifedata.com/resource/umls/id/C0004238, http://purl.bioontology.org/ontology/MSH/D001281, or http://www.conceptwiki.org/concept/index/095cb66f-76ef-41b5-a8ae-c39352e6007e

2) neXtProt nanopublications for tissue expression (PREVIEW mode) These API calls use URIs that correspond to either tissues or targets. The tissue identifiers correspond to the Caloha tissue ontology from neXtProt. These identifiers can use either the namespace from the neXtProt database (e.g. http://www.nextprot.org/db/term/TS-0564, will be operational next week) or the Caloha ontology (ftp://ftp.nextprot.org/pub/currentrelease/controlledvocabularies/caloha.obo#TS-0564, operational now).

To reduce the barriers to drug discovery in industry, academia and for small businesses, the Open PHACTS Discovery Platform provides tools and services to interact with multiple integrated and publicly available data sources. To integrate this data, extensive cross-referencing of scientific concepts is needed across all databases.

Comments

Sage mathematics software

 

Sage is a Python based free open-source mathematics software system licensed under the GPL. It builds on top of nearly 100 open-source packages: NumPy, SciPy, matplotlib, Sympy, Maxima, GAP, FLINT, R to provide a common unified interface, either as a notebook in a web browser or the command line.

In addition to a local installation it is also possible to use SageMathCloud a free service with support from the University of Washington.

I’ve added Sage to the list of data analysis tools for Mac OS X.

Comments

Medicinal Chemistry Toolkit

 

The Medicinal Chemistry Toolkit app is a suite of resources to support the day to day work of a medicinal chemist. Based on the experiences of medicinal chemistry experts, we developed otherwise difficult-to-access tools in a portable format for use in meetings, on the move and in the lab. The app is optimised for iPad and contains calculator functions designed to ease the process of calculating values of: Cheng-Prusoff; Dose to man; Gibbs free energy to binding constant; Maximum absorbable dose calculator; Potency shift due to plasma protein binding.

The app has been designed in collaboration with the editors of the forthcoming book, The Handbook of Medicinal Chemistry: Principles and Practice, which will be published in November 2014 providing a comprehensive, everyday resource for a practicing medicinal chemist throughout the drug development process and is an ideal companion for the biannual MedChem Summer school run by the RSC.

Handbook of Medicinal Chemistry_The_Publicity

Comments

Computable

 

I’ve just added Computable to the mobile science site. Computable brings iPython and SciPy to the iPad allowing to create, edit and run iPython notebooks on your iPad. Computable comes with full-featured SciPy stack, Numpy, SciPy, SymPy, Pandas, Matplotlib. The free download includes a series of 32 example notebooks and lectures that allow you to evaluate the application. To create or edit your own notebooks you will have to make an in app purchase to unlock the full feature set ($9.99).

photo

Comments