Macs in Chemistry

Insanely Great Science

Asteris, molecular design on the iPad

I’ve just finished a brief review of Asteris is a new iOS app that arose from a collaboration between Optibrium and Integrated Chemistry Design that allows medicinal chemists to design new molecules on their iPad and then calculate a range of physiochemical and ADME properties.

The complete review is here, and there is a full listing of reviews here.

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Radioactive Decay Calculator

 

I’ve just added a Radioactive Decay Calculator to the listing of mobile science applications.

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KiwiViewer

 

I’ve just added the 250th entry on the Mobile Science database, and the honour goes to KiwiViewer

KiwiViewer is a free, open-source visualization app for exploring scientific and medical datasets. KiwiViewer opens a variety of file formats and provides flexible methods of accessing data, including Dropbox, Midas, iTunes file sharing, or download via url. Supported data types include meshes, images, and point clouds, with options for vertex coloring and texture mapping. File formats include: byu, g, jpg, kiwi, mha, obj, pcd, pdb, ply, png, stl, tiff, vti, vtk, vtm, vtp, vtu, and archive formats zip, gz, bz2.

The full MobileScience database can be found here.

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Elemental updated

 

Shortly after announcing 100,000 downloads Dotmatics have posted an update to the chemical drawing app Elemental for iOS.

  • Interface tweak for iOS 7

Previous improvements - iOS 7 update - Elemental drawing bug fixes - Property prediction bug fixes - iPhone 5 support - Updated predicted properties engine - YouTube video link for introduction to the app - App size reduces from 8MB to 1MB(!) - Dropbox and Twitter Integration - Calculated Properties Panel - Rate Elemental Button! Love Elemental? Please rate us! - Follow us on Twitter button - @ElementalApp - Full Retina Display Support - File association improved - Sketched molecules persist over restarts - Copy image to Camera Roll - Copy Image to Clipboard - File association (tap and hold to load in Elemental) - E-mail attachments have been improved - support for multi-centre bonds added - Multitouch gesture support Undo - double tap Zoom - pinch Scroll - two finger drag - E-mails now export a reaction/RXN file if the sketch contains an arrow - MOL file e-mails contain predicted molecular properties: MW, MolFormula, XLogP - Add text notes into your sketch - Now compatible with iOS 5.0 and up - E-mailing of images has been improved - Larger icons

There are many other Chemical Drawing Apps that support iOS

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Asteris and RCSB PDB updated

 

The official mobile app for viewing PDB structures RCSB PDB has been updated to include the April molecule of the month.

The molecule designer app Asteris has been updated to version 1.0.1 with a number of bug fixes and performance improvements.

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Elemental for iOS

 

Dotmatics have just announced that the chemical drawing app Elemental for iOS has been downloaded 100,000 times. Whilst not in the same league as Angry Birds it surely marks an important milestone for scientific apps for mobile devices.

There are many other Chemical Drawing Apps that support iOS

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Updates to MyScript Calculator and SPRESImobile

 

A couple of mobile science applications have been updated recently.

MyScript Calculator has been given an iOS 7 makeover.

Write the mathematical expression and MyScript technology will convert symbols and numbers to digital text and delivering the result in real time.

SUPPORTED OPERATORS

  • Basic operations: +, -, ×, ÷, /
  • Powers, Roots, Exponentials: 7², √, , e³
  • Misc. Operations: %, |5|, 3!
  • Brackets: ( )
  • Trigonometry: cos, sin, tan, cot, cosh, sinh, tanh
  • Inverse trigonometry: acos, asin, atan
  • Logarithms: ln, log
  • Constants: π, e, phi.

SPRESImobile has also been updated, there a number of bug fixes and you can now search by reaction name.

SPRESImobile provides you with a powerful and convenient way to access ChemReact, containing around 410,000 chemical reactions and related references. InfoChem created ChemReact for chemists who need information about effective reaction transformations. We achieved this by selecting representative examples of each reaction type from the larger SPRESI data collection of 1974-2009.

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Asteris

We are starting to see companies exploit the client server model in bringing ever more sophisticated scientific applications to the iPad.

Asteris is a joint development from Optibrium the creators of StarDrop and Integrated Chemistry Design who created Chirys Draw. Asteris uses Chirys Draw’s touch interface to design novel molecules and then uses StarDrop’s predictive modeling power, guided by the Glowing Molecule™ visualization, instant feedback dramatically reduces the time it takes you to identify high quality compound designs. Using Asteris you can calculate a range of simple “core properties”, and ADME properties, including solubility, hERG inhibition and CNS penetration, using rigorously validated models from the StarDrop platform.

  • CORE PROPERTIES
  • Molecular Weight
  • Number of rotatable bonds
  • Flexibility
  • Number of hydrogen bond donors
  • Number of hydrogen bond acceptors
  • Topological polar surface area.
  • logP
  • STARDROP ADME PROPERTIES
  • logS
  • logS7.4
  • logD
  • 2C9 pKi
  • hERGpIC50
  • BBB log([brain]:[blood])
  • BBB category
  • HIA category
  • P-gp category
  • 2D6 affinity category
  • PPB90 category
asteris

All of the predictions are calculated using StarDrop ’s ADME QSAR module. You will need to be connected to the internet to perform these calculations using the secure Asteris cloud server.Alternatively, you can run the calculations on your own server with the “Enterprise” edition.

All communications with the server uses industry-standard SSL encryption. No compound structures or data are stored on the server. Calculate "core properties" for an unlimited number of molecules for free. Calculate ADME properties for 20 new compounds each month, free of charge. Additional ADME property calculations can be purchased via an in-app purchase.

There are demo videos on the support site.

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Papers3 for iOS updated

 

Whilst Papers3 remains an extremely popular desktop reference management application Papers3 for iOS has come in for some criticism, in particular poor synchronisation with the desktop and the use of unintelligible file names. The latest version seems to address some of those concerns.

What's New in Version 3.1.5 New:

  • Supplemental file support.
  • Sharing PDFs via email now use human readable file names.

Stability fixes:

  • Fixes a crash related to syncing.
  • Improved performance on syncing.

Other:

  • General bug fixes.
  • Improved general appearance on iPhone.

The Mobile Science website contains more science apps for iOS.

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MobileScience First quarter review

 

Since it has been just over three months since I built the Mobile Science website I though it might be interesting to see how it is performing. After a slow start there have been around 6000 page views and looking at the weblog it is clear many people are starting to use the search facilities to explore. Currently there are around 250 scientific apps listed and I’ve started to add iOS programming resources.

The top 25 viewed apps are:-

Wolfram|Alpha
Papers for iOS
ChemDoodle Mobile
The Elements in Action
ChemDraw for iPad
Elemental
iMolView
The Elements in action
Play to cure: Genes in Space
Living Molecules
iOS Chart Library
Chemistry by Design
TouchPlot
Learn NMR FID
SciVerse Science Direct
Mobile HyperChem
Mobile Molecular DataSheet Toolkit
Reaction 101
Mathematics with PocketCAS pro
RCSB PDB Mobile
Tydlig - Calculator Reimagined
PyMOL
ElementalDB
Plasmid.io
Named Reactions Pro

Whilst the number of chemistry apps is perhaps unsurprising it is great to see other areas of science starting to make an appearance.

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ACS Meeting Spring 2014 mobile app

 

The ACS Mobile Meeting Application is your full featured guide to manage your experience at the 247th ACS National Meeting & Exposition in Dallas, TX. App features include: - Native app: No wifi connection required to access the conference program, schedule, or maps. - Home: Quick access to technical, social, and governance meeting program browse and search features, exposition information, and app user guide. - Program: Browse the entire event program to build your personal schedule, bookmark sessions or speakers, or access session handouts as available. - Take notes and share them via email. - Connect your meeting experience with social media. - Exhibitors, Maps, related conference info and much more

There many more mobile application on the MobileScience website.

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RCSB PDB Mobile Updated

 

RCSB PDB Mobile has been updated to include molecule of the month.

There is a comparison of Molecule Viewers for iOS here.

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Molecule Viewers for iOS

 

I’ve put together a page briefly describing the molecule viewers I’ve found for iOS.

I’ve included both small molecule and large biomolecule viewers, together with some that use a client server model.

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Brian Cox and the wonder of Life

 

Everyones favourite physicist Brian Cox has just brought out a new app. The wonder of Life app allows you to explore nature in 3D with Professor Brian Cox as your personal tour guide. This is a follow up the highly successful Wonders of the universe.

Brian Cox is an excellent presenter and these apps are based on the highly successful BBC TV series, Wonders of Life and Wonders of the Universe.

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TB Mobile Updated

 

TB Mobile from Collaborative Drug Discovery been updated.

TB Mobile makes available a set of molecules with activity against Mycobacterium Tuberculosis, and known targets available in CDD. It links to pathways (biocyc.org), genes (tbdb.org), literature (PubMed).

The latest update adds support for iOS7, and adds further compounds and molecular targets. So now there are 96 unique targets and 805 compounds. There is also major new functionality including interactive clustering, personal favourites, target prediction and exporting capabilities.

tbmobile

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Spectroscopy apps for iOS

 

I’ve just been sent details of a number of iOS apps that would be useful to those involved in spectroscopy, (NMR, IR, MS) so I’ve added them all to the mobile science site.

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Learn NMR FID

 

Learn NMR FID is a great teaching tool to learn the basics of NMR data collection and processing. Use simulated free induction decays (FIDs) and spectra to see apodization, noise and relaxation effects. Move peaks and see how the FID changes. Real and imaginary FIDs prior to and after processing are displayed as is the resultant spectrum after the Fourier transform.

There are more science apps for iOS on the mobilescience site.

I also thought I’d mention this framework that was brought to my attention recently. There is a trend to move massively parallel tasks to the GPU, GPU Image is a framework (BSD license) that simplifies the creation of GPU filters. This framework is built around OpenGL ES 2.0, so it will only work on devices that support this API. This means that this framework will not work on the original iPhone, iPhone 3G, and 1st and 2nd generation iPod touches. All other iOS devices are supported.

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Play to Cure™: Genes in Space

 

Beating cancer through a space game never seemed possible. Until now….

Every day, scientists across the globe are painstakingly analysing the genetic faults in thousands of cancer samples. They are looking for clues that will help develop new cancer treatments. This game let’s you help.

Play to Cure™: Genes in Space is a pioneering way of helping these scientists in their mission to beat cancer sooner and all via this world first mobile game supported by Cancer Research UK.

A mysterious substance is discovered in the voids of deep space. Dubbed Element Alpha, the substance is refined for use in medicine, engineering and construction and soon the Element Alpha industry explodes galaxy wide.

As an employee of Bifrost Industries, one of the biggest traders of the substance, your job is to collect as much Element Alpha as you can and trade it for upgrades to your spacecraft to help you manoeuvre the asteroid filled space course.

Game features:

  • Arcade/action space gameplay
  • Rise through the ranks at Bifrost Industries from Recruit to Galactic Legend
  • Upgrade and customise your ship with unique items, weapons and colours
  • Plan your route to maximise your Element Alpha haul
  • Maximise your profits by trading your Element Alpha when the market is high or sell immediately for a guaranteed return

HOW THIS HELPS TO BEAT CANCER SOONER

Element Alpha represents genetic cancer data that scientists across the world analyse on a daily basis. Genes in Space has successfully translated this data into an interactive, asteroid-strewn intergalactic assault course.

By collecting Element Alpha and navigating your spaceship through the cosmos you’re finding the significant genetic changes which help scientists to discover cancer causing genes and develop new life saving treatments.

So gamers take note. The Genes in Space story may not be real, but the impact of what you’re doing is far from science-fiction.

Why not download Play to Cure™: Genes in Space and do your bit.

This application is designed for iPhone 4S and higher, along with iPad 2 and higher. You can play on older devices but your gaming experience may not be the same

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Wolfram|Alpha has been updated

 

The Wolfram|Alpha iOS app has been updated. This is an essential app whether or not you are a scientist.

This update fixes a few bugs and supports iOS7 design.

There are more apps on the MobileScience website.

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SVGgh

 

I’ve just added SVGgh from GenerallyHelpfulSoftware to the MobileScience website.

SVGgh is a collection of classes for using SVG as artwork in iOS Apps. Includes a UIView and a button class.

No excuse for using bit mapped images!

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Papers3 for iOS Updated

 

I see that Papers3 for iOS has just been updated to version 3.1.1.

This version now includes article level metrics (Altmetrics) on the article you're reading now available in the landmarks view (PDF reader).

  • General bug and stability fixes.

  • Improved performance on syncing.

There are more science apps for iOS here http://www.macinchem.org/mobilescience/.

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FierceBiotech and FiercePharma added to mobile science

 

I’ve just added FierceBiotech and FiercePharma to the MobileScience website. Those are two very popular industry news monitors.

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Circus Ponies Notebook

 

A while back I was asked to help with an Applescript to help automate the transfer of notes from an iPad to Evernote on the desktop. Since then I’ve kept an eye on the increasing interaction between mobile device and desktop. It is clear that more and more applications now have versions that run on the iPad allowing you to access information on the move. I noticed a recent review of Notebook from Circus Ponies that again emphasises the importance of the iPad version that automatically syncs with the Mac version.

I’ve never been on a business trip without my MacBook Pro but I wonder if we are getting close?

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Wolfram|Alpha and chemistry homework problems

 

There is an interesting post on Molecular Modeling Basics on the use of Wolfram Alpha to solve chemistry homework problems. I have to say I continue to be impressed by Wolfram Alpha, the breadth and depth of science that is covered is amazing.

For science apps for iOS have a look at the mobile science page.

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Anaglyph 3D now available in iMolview

 

I was just reading the end of year newsletter from [Molsoft] and I came across this interesting snippet.

MolSoft is excited to announce that Anaglyph 3D is now available to use in ICM and iMolview.

Sure enough the update on Dec 24th has this in the release notes.

Anaglyph stereo mode is added. (Set 'Stereo Type' to 'Anaglyph' in Tools menu) Any red-cyan 3D glasses will work in this mode.

There are a number of suitable glasses on Amazon 3D Red/Cyan Glasses

I think this is the first app to enable this sort of stereo viewing and it just underlines the strides that mobile platforms are making in scientific computing.

For science apps for iOS have a look at the mobile science page.

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iOS7 Tech talks

 

The iOS7 tech talk videos are now online.

Registered Apple Developers can watch full sessions from the iOS 7 Tech Talks to get in-depth guidance on developing for iOS 7. Discover how to create innovative, flexible, and intuitive apps that integrate the latest Apple technologies.

ios7

For science apps for iOS have a look at the mobile science page.

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Mobile Science Website

It has been just over a month since I set up the Mobile Science database and I thought it would be good to have a look at how things were going. The aim of the database was to enable scientists to be able to search for scientific apps for iOS.

It took a lot of work to compile all the information so I’m delighted to see that it has been accessed nearly 1500 times with visitors from all over the world. A fair number of people have been voting for their favourite application and it perhaps not surprising that the chemical drawing applications, Elemental, ChemDoodle Mobile and ChemDraw are all in the top 5. The other apps picking up votes are popular scientific search and computation tool WolframAlpha and the award winning reference management app Papers3, together with ElementalDB an app that allows you to search a local copy of the 1.2 million record ChEMBL database, an app that really demonstrates the computing power now available in a hand-held device.

I will of course continue to update the database but since finding science apps on the iTunes Store can be a challenge I’d be delighted to hear about any that I have missed.

elemental

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The Elements in Action

 

Originally Theodore Gray produced a beautiful coffee table book The Elements: A Visual Exploration of Every Known Atom in the Universe, this was later converted into an iPad app The Elements which gave access to more dynamic information than could be achieved with a hard copy book. Now the developers have gone one step further and created The Elements in Action a periodic table with video explorations of the properties of elements. Some of the videos look like they have been rescued from old research labs so this is probably your only opportunity to see them in action.

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Mobile science app updates

 

A couple of applications from Molecular Materials Informatics, Inc have been updated.

Open Drug Discovery Teams is a content management system providing crowd sourced information on a range of tropical and neglected diseases. The ODDT app is free. It can be used anonymously to browse topics. Submission of content requires the user's Twitter account to be enabled and made available to the app.

ODDT

Living Molecules allows specially crafted molecular glyphs to be snapped by the device camera, which direct the app to chemical data: molecules, reactions and collections. This update fixes a bug that could cause the app to crash.

Mobile Molecular DataSheet update includes Sketcher improvements: crayon gestures for adding rings and lines; traversal gesture for growing rings from bonds; and a "band-aid" feature for fixing badly drawn chain bonds.

There is now a searchable database of mobile science apps

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Chem3D and ChemDraw for iPad updated

 

Both ChemDraw and Chem3D have been updated, the release notes don’t give much information on the updates other than Redesigned for iOS7 and bug fixes.

The use of mobile devices in teaching has offered new opportunities and a recent presentation by Layne Morsch illustrates this quite nicely. Using ChemDraw for iPad and Flick-to-Share to Increase Engagement in Organic Chemistry. The page has a couple of embedded videos that give more details.

The other feature that is now becoming mainstream is the 3D-printing and since Chem3D can export in .stl format it is not surprising people have started to experiment with creating 3D models of molecules, there is a brief video here, unfortunately it is a loop of the printing process so don’t expect to see the final product. CambridgeSoft have also produced their own videos of these apps in action

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Mobile Science App updates

 

A couple of apps have been updated recently

WolframAlpha the world's definitive source for instant expert knowledge and computation.

Living Molecules allows specially crafted molecular glyphs to be snapped by the device camera, which direct the app to chemical data: molecules, reactions and collections

There is now a database of mobile science apps

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iOS programming

 

As the MobileScience site expands I’ve started to add other resources in addition to the applications. There are now a couple of useful additions for iOS programmers if you are looking for a training course, a plotting library or a chemistry toolkit.

I’d be delighted to add any more useful resources.

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MobileScience Apps

Finding scientific applications for your iPhone to iPad has always been a little hit and miss since there is no “science” category on the iTunes store. To help out I created a page listing applications that I knew about, unfortunately as the number of applications increased the page became unmanageable. In addition an alphabetical listing is not the most useful way to search through them.

I’ve now transferred all the information to a database that can be searched via a web interface.

mobsci

The site is available at http://www.macinchem.org/mobilescience/, I’ve started to categorise applications to aid navigation but I’d be interested to hear of any suggestions. Currently there are over 200 entries covering an extensive area of science, if I’ve missed any please let me know and I’ll add them.

In the news section I’ve added links to publications and presentations that might be interesting.

I’d encourage to have a look around and I’d be interested to hear any comments or suggestions.

 

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Experimental Assistant

 

Experimental Assistant from Nano3D Biosciences. This application helps organize and analyze data from experiments. It take manual photos and automatic shooting for multiple images and time lapse movies, and stores them in albums for easy access later

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ChemDraw and Chem3D for iPad updated

 

There are updates to both ChemDrawand Chem3D) for iPad. There is little information available about the update to version 2.0 other than “bug fixes” and the apps have been redesigned for iOS7 and now have a minimum requirement for IOS7.0 or later.

c3dipad

The mobile science page contains a listing of science apes for iOS.

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Mobile security concerns

 

I’m hearing more and more concerns about security concerns with regard to mobile devices. I guess this was to be expected as more people have smart phones and tablets start to replace laptops. It seems Google's executive chairman Eric Schmidt drew laughter when discussing security on the Android platform, Executive chairman dances around straight answer while talking up Android security.

Schmidt said in the distant future there would be an assumption that nothing is secure and that security will be devised on a per app basis for each user.

I’m not sure whether many people would find that situation very helpful. His view is perhaps a consequence of a recent study issued by the Department of Homeland Security (DHS) and the Federal Bureau of Investigation (FBI) suggesting Android devices represent a significant security threat. Of the malicious attacks documented in the study, 79 percent took place on an Android device and 19% on Symbian whilst Apple's iOS received just 0.7 percent of the recorded malware threats. One of the key sources of threats appear to be the installation of apps from insecure sites, so whilst the approval process for the Apple iTunes store occasionally causes complaints it also acts as a significant security barrier. Whilst the Google Android should have the same role it is perhaps worrying to find that recently 50 malicious apps had to be removed. There have however now been reports of threats distributed via email spam.

The Android trojan known as Stels began distributing via fake U.S. Internal Revenue Service-themed emails, using an Android crimeware kit to steal sensitive information from the device, and monetizing by making calls to premium numbers.

Apple does seem to be taking the security concerns seriously, the AppStore provides an initial check on apps, the new fingerprint authentication provides an extra level of device protections. In iOS7 we have Activation Lock so that someone who’s got hold of your device can’t disable Find My iPhone without knowing both your Apple ID and that Apple ID’s account password. The person with your lost device can’t erase data on the device, also if you designate your device as being lost it can’t be restored to reactivate it—the phone displays only a phone number and a custom message about contacting you.

Keeping the operating system up to date helps, and the adoption rate for iOS7 is very impressive.

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iOS7 Adoption rate

 

I was just looking at the iOS7 adoption rate on the Mixpanel website. When I looked last night, iOS7 stood at 63% of users, iOS6 just over 32% with older versions of iOS below 4%. Given that iOS7 has only been available just over a week this is a remarkable adoption rate. Excellent news for all those mobile science developers since it looks like will be able to focus their efforts on the latest version of the operating system,.






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Labguru

Labguru this is a mobile app for iPad, iPhone and iPod, a complement to your Labguru account, Labguru Mobile assists you with 4 essential functions: Record images of results and link them to their specific experiment, Drill down into your lab's storage locations, Manage orders and inventory with the shopping list, Retrieve protocols on your bench to execute experiments then automatically integrate results into your Labguru account

Now added to the mobile science page.



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PhySyCalc

PhySyCalc is an interesting scientific calculator that lets you do full calculations but also lets you include the units. It also includes many useful mathematical functions, as well as a number of useful physical constants. Included also are the speed of light, and the mass of the electron, proton, and neutron, all with appropriate units, atomic weights, isotope weights, and isotope abundances.

GasConstant

PhySyCalc features include:

  • Intuitive, minimal buttons in portrait display for ease and speed of use
  • Quantity units supported in all calculations
  • Calculations entered in full before evaluating
  • Use of parenthesis within your calculations
  • Full featured scientific calculator
  • Left swipe display for unlimited undo. Makes it easy to find mistakes and correct them.
  • Right swipe display for redo
  • Two finger slide on display to reduce the number of significant figures
  • Complex numbers

Now added to the Mobile Science Page.



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Choosing the app to view a file.

I mentioned in my ChemDraw for iPad review that you could open files in DropBox and I had a couple of people ask how.

With the DropBox app installed if you navigate to a file and click the icon in the top right corner you get a drop down menu asking which application to open a file with.

photo



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ChemDraw and Chem3D for iPad updated

I just noticed that there are a couple of updates on my iPad, in particular ChemDraw and Chem3D for iPad have both been updated. What is particularly appealing is that they certainly seem to be listening to their users with several of the top requested features now being incorporated. I’m particularly delighted to see DropBox fully integrated as a sharing capability, for a mobile device this is absolutely critical. At the moment you can upload CDXML, PNG or PDF file formats, and you can only save to a ChemBioDraw folder within DropBox. Perhaps unsurprisingly social media outlets (Twitter and Facebook) are now also supported.

Chem3D now has the ability to pull more structures from public databases, perhaps in the next update of ChemDraw we might see the ability to pull structures from public databases such as ChemSpider?

The ability to add text boxes to structures and schemes will be very useful and will make this a more useful app for note taking. The default text seems to be Times New Roman but you can change text style using the “Colours and Styles” button. The ACS template is now available, but you can’t use your own templates.

ChemDraw for iPad 1.0.2 Features

  • Text capability to annotate structures and reactions (single-most requested feature in product reviews)
  • Adjustable arrows (another top requested item)
  • More sharing capabilities including DropBox, Twitter, Facebook, and Moxtra
  • Group Flick-to-Share (based on our summer pilots and geared toward educators)
  • Orbitals, brackets
  • Two categories of templates (structures)
  • Enhanced periodic table keyboard capabilities including an ability to quickly type a chemical formula
  • American Chemical Society template
  • Simplified Chinese language support
  • Korean language support   Chem3D 1.0.2 Features

  • More sharing options including DropBox, Twitter, Facebook and Moxtra

  • Ability to pull in more structures (PDB and CIF) from public databases including now by keyword search for structure or author
  • Group Flick-to-Share capabilities
  • Simplified 3D printing output (now via DropBox or email)
  • Simplified Chinese language support
  • Korean language support

These are excellent updates and well worth installing. A minor comment since Chem3D can import PDB structures from public databases, it might be nice to be able to save them in PDB format.

I’ve updated review I wrote.



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Mobile Science Page Updated

I’ve updated the mobile science page adding a few new applications.

3D Molecules Edit&Drill is designed to enable students to build, construct, modify and examine molecules in 3D.

CueMol viewer for iOS is an interactive macromolecular viewer for structural biologists. CueMol viewer allows the users to open and view the scene files made by the desktop version of CueMol, and the Protein Data Bank (PDB) format files, as well.

GLmol Free and open source 3D molecular viewer based on WebGL and Javascript. GLmol runs on newer versions of Firefox, Chrome, Safari or Opera. Internet Explorer is not supported. GLmol also runs on WebGL enabled safari in iOS.

iPharosDreams is a molecular visualization app for iPad that allows you to perform in-silico drug discovery. This app basically has functions that download protein structure files from Protein Data Bank, display 3D molecules, touch, rotation, zoom in/out. Hierarchy structure of molecules is shown with a table that select precisely components in a protein and related things. Above all, you can generate pharmacophores and analyze 3D protein-ligand interaction of biological macromolecules for in-silico drug discovery. You can select a ligand from a protein and generate a binding site from the selected ligand. From the binding site, also you can generate receptor based pharmacophores and get inspiration for good hit compounds interact with the protein well.

Many thanks to those who suggested links.



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ChemDoodle Updates

IChemLabs have announced a couple of updates

ChemDoodle Web Components 5.2.2 has been released, this is a minor update This update fixes some issues, and most notably stabilises the WebGL text system. They have updated a few of the demos to show off this feature:

2D to 3D Coordinates
MolGrabber 3D
PDB Ribbons

ChemDoodle mobile 1.4.1 is also now available from the App Store, the release notes include.

  • Support for the iPhone 5
  • IUPAC Naming
  • 3D coordinate generation and viewer
  • Added empirical formula to calculations
  • Added rotatable bond count to calculations
  • Added total electron count to calculations
  • Added vdW volume to calculations
  • Added complexity to calculations
  • Fixed slow performance issues on iPad in landscape mode
  • Fixed MolGrabber search issues
  • Fixed issue where the back button wouldn’t appear on the last help page
  • Fixed login issues
  • Performance improvements
  • General improvements and fixes



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Mobile Science apps

I’ve already mentioned ChemDraw for iPad but Perkin Elmer also released Chem3D for iPad yesterday, it should be noted that Chem3D for iPad is a simple molecule viewer and it does not include the computational abilities of the desktop version.

Both are now included on the mobile science page



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ChemDraw for iPad

About three decades ago I stopped using a stencil and a Rotring pen to create chemical structures for publications and started using ChemDraw on a Mac, at the time it transformed the standard of structures in publications and it has continued to set the standard for publication quality chemical structures. Over the years the software has developed and moved into cheminformatics, spectroscopy and more recently biological drawing. This lead to the rebranding as ChemBioDraw but most of the chemists I know still call it “ChemDraw”. So it is perhaps not surprising that I feel rather pleased that the iPad version is entitled simply ChemDraw.

You can read a full review here.



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Living Molecules Updated

The Living Molecules iOS app has been updated, this version now activates the phones flashlight to better capture the glyphs in dim conditions.

The Living Molecules app allows you to turn chemical structures into a molecular glyph, which can be used on documents like posters, manuscripts or web pages. Anyone who has the app can use the camera to capture molecular glyphs, and bring the chemical data onto their device. A molecular glyph is the chemical equivalent of a QR code.



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JSME: a free molecule editor in JavaScript

Another javascript-based molecular editor JSME was recently described in the Journal of Cheminformatics, JSME is a port of the very popular JME java applet.

The actual molecule editing Java code of the JME editor was translated into JavaScript with help of the Google Web Toolkit compiler and a custom library that emulates a subset of the GUI features of the Java runtime environment. In this process, the editor was enhanced by additional functionalities including a substituent menu, copy/paste, drag and drop and undo/redo capabilities and an integrated help. In addition to desktop computers, the editor supports molecule editing on touch devices, including iPhone, iPad and Android phones and tablets. In analogy to JME the new editor is named JSME. This new molecule editor is compact, easy to use and easy to incorporate into web pages.



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Living Molecules

The Living Molecules app allows you to turn chemical structures into a molecular glyph, which can be used on documents like posters, manuscripts or web pages. Anyone who has the app can use the camera to capture molecular glyphs, and bring the chemical data onto their device. A molecular glyph is the chemical equivalent of a QR code.

glyph

The glyph contains just enough information to establish a source and identification for the data, so that the content can be downloaded from the internet and viewed:

livingmolecules

I’ve been trying this out over the weekend and whilst it works, it looks like it is very resource intensive and my old iPhone 4 really struggled. This looks like an interesting project and it will be interesting to see how it develops.

I’ve added it to the list of mobile science applications.



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The Portable Chemist's Consultant

This is the first major scientific text that I’ve seen that specifically aims for the iPad rather than hardback books, and I suspect it will become the norm in the future. When scientific text books are so expensive, and need regular updates this becomes a very attractive model. The Portable Chemists Consultant

This is a chemistry book like no other. This is your virtual consultant. If you work in any chemical company, our aim is to make this your survival guide. This is your portable consultant, available 24/7, and offering advice that cannot be obtained by cursory use of search engines. This consultant doesn't charge an hourly rate, has no ego, and is being constantly updated and improved upon. At no additional cost. In Part 1, The Portable Chemist's Consultant places particular emphasis on heterocyclic chemistry since this is the bedrock of society-shaping materials such as medicines and agrochemicals. Beautiful interactive graphics are designed to rapidly solve your problems by being both immersive and rapidly absorbed. In Part 2, a broad coverage of solutions to the most encountered problems and issues of industrial chemists is presented

chemcompanion



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ElementalDB Updated

I just noticed an ElementalDB update appear on my iPad.

According to the release notes there have been substructure search performance improvements.

ElementalDB allows you search and explore the 1.2 million structure CHEMBL database locally on your iPad.

There is a review here.

photo



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ChemDoodle Mobile Updated

I just noticed that an update for ChemDoodle was available on my iPhone.

According to the release notes this includes

  • Support for the iPhone 5
  • IUPAC Naming
  • 3D coordinate generation and viewer
  • Added empirical formula to calculations
  • Added rotatable bond count to calculations
  • Added total electron count to calculations
  • Added vdW volume to calculations
  • Added complexity to calculations
  • Fixed slow performance issues on iPad in landscape mode
  • Fixed MolGrabber search issues
  • Fixed issue where the back button wouldn’t appear on the last help page
  • Fixed login issues
  • Performance improvements
  • General improvements and fixes

There is a page of mobile science applications here.



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ElementalDB on AppStore

ElementalDB is now available on the AppStore.

https://itunes.apple.com/app/elementaldb/id627422287

Sketch and search within the 1.2M compound ChEMBL 15 dataset. Searching, property calculation and depiction is done from the stored 2D co-ordinates from ChEMBL within the app on your device



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TB Mobile

There is an interesting article in the Journal of Cheminformatics regarding an app I’ve highlighted previously, TB Mobile: a mobile app for anti-tuberculosis molecules with known targets.

TB Mobile may assist researchers as part of their workflow in identifying potential targets for hits generated from phenotypic screening and in prioritizing them for further follow-up. The app is designed to lower the barriers to accessing this information, so that all researchers with an interest in combatting this deadly disease can use it freely to the benefit of their own efforts.

tbmobile

There are more mobile science applications listed here.



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Four new mobile science apps

Four new mobile science applications from ZappyLab a provider of mobile and web applications for scientists. They focus on creating tools that are helpful to researchers and laboratory workers.

GrowthCurves is a portable spreadsheet for researchers working with cell cultures.

PubChase is a science literature search and recommendation tool, available online or on your mobile device

Lab Counter is a tallying app, specifically designed for the scientists and medical laboratory workers.

Tetrad is a utility for yeast geneticists to score yeast tetrad dissections.

They have all been added to the mobile science page.



Comments

SAR Table updated

The SAR Table app has had the ability to match scaffolds to molecules for a while now, but as of the latest release (1.3.4) just submitted to the AppStore, it will be able to match more than one scaffold at once. The actual process of performing the scaffold match is provided by a webservice (molsync.com).

More details here.



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Molecule Calculator

After I wrote the article about javascript based molecule viewers I’ve been sent a couple of links demonstrating their use. One particularly interesting one is MolCalc an online molecular calculator that uses JSmol to build and render structures.

molcalc1

Once the molecule has been built and minimised using the MMFF force field you can then use GAMESS to calculate a range of molecular properties.

molcalc2

MolCalc is distributed through GitHub under the GPL license github.com/jensengroup/molcalc. You must obtain a copy of the GAMESS code separately from www.msg.ameslab.gov/gamess/download.html Since this uses javascript for the interface it will work on mobile devices.



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Elemental for iPad/iPhone updated

Dotmatics have announced an update to their chemical sketching application Elemental to version 1.5. No details of any changes are available.

There is a page of mobile science applications here.

Chocolat a text editor for Mac OS X, that combines native Cocoa with powerful text editing tools has been updated.

There are more text editors here.



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Green Solvents updated

The latest version of Green Solvents (1.1) is now available on the AppStore. Worth noting is the fact that the app is now sponsored by the Royal Society of Chemistry.

There is a page of mobile science applications here.



Comments

Elemental for iPad/iPhone updated

Dotmatics have announced an update to their chemical sketching application Elemental. Version 1.4 includes an improved calculated properties engine.

photo

There is a page of mobile science applications here.



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A busy time for mobile science

There are a couple of things happening in the mobile science space that I thought I should highlight.

The SAR Table app is going through some major improvements at the moment. The recently added matrix view is being modified to make it more interactive.

sartable

Recently the Mobile Molecular DataSheet (MMDS) was updated with the ability to parse ChemDraw files in particular it understands reaction schemes.

It can extract reaction schemes, and reassemble them into the more highly structured form that MMDS uses, i.e. segregated into individual components, where each distinct part of the reaction is characterised as a reactant, reagent or product, and is described by name/structure/both, and stoichiometry.

The ChemSpider synthetic pages reactions are stored in Chemdraw format and can thus be imported into MMDS, the sequence of actions is shown here

There is also a presentation by Antony Williams describing work at the Royal Society of Chemistry to support mobile science.



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The continued rise in mobile computing

The latest data from Net Applications is available and the continued rise in mobil computing is clearly seen. In January 2013 mobile devices account for nearly 12% of web usage, with iOS holding just over 60% and Android 24%. Blackberry languishes at under 2% and it remains to be seen whether there new offerings will revive the once market leading company. The iPad is the most popular mobile device followed by iPhone.

On the desktop it is pretty much unchanged, Windows still account for around 90% (with XP unchanged at 39%) and Mac just over 7%. Mac OS X 10.8 is the most popular Mac operating system.

There is a page of mobile science applications here.



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SPRESImobile updated

With SPRESImobile, a wealth of chemical reaction information is readily available at your fingertips from a mobile device (iPhone, iPad). You can search the entire ChemReact database easily with this highly intuitive app

There is a page of mobile science applications here.



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Mobile Molecular DataSheet Updated

I just noticed that version 1.4.1 of the Mobile Molecular DataSheet (MMDS) has just been submitted to the iTunes AppStore, and its notable new feature is the ability to select a datasheet and calculate structure-based properties. A new column is created for each selected property, and the calculation feature is applied to each row. The available properties currently include molecular weight/formula, log P, molar refractivity and topological polar surface area. The functionality is provided by the molsync.com webservice.

There is more information on the Cheminformatics blog.

There is a page of mobile science applications here.



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Search integration added to MolPrime+

Database searching has now been added to MolPrime+ for iOS. The latest version, 1.1, has been submitted to the AppStore and should be available soon. As soon as it is approved, it will be possible to easily search the PubChem and ChEBI databases, by name or structure, and use the results within the app.

molpp_search1

There is a detailed description here

There many more iPhone/iPad apps on the mobile science page.



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Cheminformatics workflows using mobile apps

Yet another publication describing the impact of mobile science.

We are perhaps at a turning point for making cheminformatics accessible to scientists that are not computational chemists. The proliferation of mobile devices has seen software or ‘apps’ developed that can be used for sophisticated chemistry applications. These apps can offer capabilities to the practicing chemist that are approaching those of conventional desktop-based software, while still apps tend to be focused on a relatively small range of tasks. Mobile apps that can pull in and integrate public content from many sources relating to molecules and data are also being developed. Apps for drug discovery are already evolving rapidly and are able to communicate with each other to create workflows, as well as perform more complex processes, enabling informatics aspects of drug discovery (i.e. accessing data, modeling and visualization) to be done anywhere by potentially anyone. We will describe how these cheminformatics apps can be used productively and some of the future opportunities that we predict.

There is a page of mobile science applications here.



Comments

Green Solvents

Mobile science continues to make inroads, this publication describes the work to make Green Chemistry information more accessible.

Incorporating Green Chemistry Concepts into Mobile Chemistry Applications and Their Potential Uses DOI

There is a page of mobile science applications here.



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Structure activity on an iPhone

An interesting post on Cheminformatics 2.0

the SAR Table app has a not-yet-released feature which allows the current set of structures and their activities (“responses”) to be packed off to a webservice, which proceeds to construct a model based on structural features, then predicts values for any structures that don’t have values for that particular property.

Mobile science is coming on in leaps and bounds.

There many more iPhone/iPad apps on the mobile science page.



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StructureMate

Datasets are ubiquitous in chemistry research and education. For fields involving organic chemistry, these datasets often take the form of Structure data files (SD files). Although an assortment of tools can present SD files on desktops and laptops, few options exist for doing so on increasingly-useful tablets and phones StructureMate™, aims to bring chemical structure dataset analysis and visualisation to a much wider range of devices. This Universal app runs on both the iPad/iPad Mini and iPhone/iPod Touch families, with custom-built interface for each.

structuremate-iphone

There many more iPhone/iPad apps on the mobile science page.


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Tableau Mobile

A few days ago I mention Spotfire for the iPad and a couple of readers sent in details of similar applications.

Tableau mobile is an iPad front-end to an analytics server. Create interactive reports and dashboards in Tableau Desktop then publish them to Tableau Server for secure access on your desktop, or on the web or with your iPad.

Similarly SAP BusinessObjects Mobile connects to the SAP BusinessObjects Business Intelligence platform.

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Spotfire for iPad

Spotfire for the iPad requires access to a TIBCO Spotfire Web Player Server. By default, the app is connected to our public demo gallery so you can start experiencing data in Spotfire immediately. After that, you can connect to your internal server, or you can connect to public servers and explore Spotfire analytical tools.

spotfire

Now added to the mobile science page.

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BioGPS

BioGPS free extensible and customizable gene annotation portal, a complete resource for learning about gene and protein function.

biogps

Now added to the mobile science page.

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Xcode updated

With the release of the iPad mini Xcode has been updated to version 4.5.2 this update includes:-

Support for iPad mini and iPad with Retina display (4th generation).
Additional bug fixes and stability improvements.

Xcode 4.5 includes

  • SDKs for OS X 10.8 Mountain Lion and iOS 6.
  • Auto Layout now supported on both OS X and iOS.
  • New localization workflow can share a single base .xib or .storyboard file for multiple locales.
  • OpenGL debugger for iOS analyzes performance and suggests improvements.
  • Debugger watchpoints can be set when running on a connected iOS device.
  • Objective-C @synthesize command is generated by default when using properties.
  • Objective-C adds literal syntax for numbers, arrays, dictionaries, and expressions.
  • Xcode 4.5 runs on both OS X Lion and OS X Mountain Lion.
  • Enhanced for the MacBook Pro with Retina display.

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A collection of mobile science apps

Labguru for iPad is a companion app to the Labguru web application. The app enables Labguru users to conduct and update their experiments from the lab bench. The app makes it possible to run and track multiple experiments, record notes and results while performing an experiment, and to sync the data with the Labguru web application.

My Lab, your iPAD is now a lab notebook, protocols organizer, lab inventory and much more. My lab was conceptualized and developed under the scientific expertise of Mahendra Rao MD PhD and Hue Medscience. My lab is a customizable app that lets you keep your lab data private and enables sharing of the content you want enabling full control of your files. My Lab also includes direct access to Dropbox to store your files for easy access from anywhere

BioTechniques The International Journal of Life Science Methods – Now on Your Mobile Device BioTechniques provides open access to high-quality, peer-reviewed papers on laboratory techniques and protocols. Now in its 52nd volume, BioTechniques has over 80,000 print subscribers worldwide.

Oracle Oracle Business Intelligence Mobile for Apple iPad and Apple iPhone is a mobile analytics application that allows users to view, analyze and take action on Oracle Business Intelligence content.

The Journal of Cell Biology app allows immediate access to full-text articles. The original international cell biology journal, JCB now travels wherever you do. You can read full-text articles anywhere at anytime, even without a network connection. The app, designed for easy reading and browsing on any iOS device

Life Technologies Protocols App provides quick, convenient access to popular Applied Biosystems or Invitrogen product protocols. Each protocol is presented with concise step-by-step instructions, along with easy access to the complete product manual

PNAS, the official journal of the US National Academy of Sciences, is an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences. The journal is published daily online in PNAS Early Edition and weekly in print. Easily access the PNAS table of contents and full text articles directly from your mobile device.

Mol Biology Get all the latest research findings from Molecular Microbiology, including articles yet to be published in an issue. Our iPad-optimised design provides the best browsing experience possible. With a few simple clicks you can quickly and easily move between articles, images and more.

MIQE - qPCR helps you in reviewing scientific works and checking your own experiments, when qPCR is involved. Check your project's compliance to MIQE in minutes, have all required references to hand, and follow qPCR events and new

Cell Imaging HD This mobile app is designed to help you find fluorescent dyes, reagents and protocols for cell biology related fluorescence microscopy applications.

BioLegend Tools , this application provides you with important information about your mouse and human CD Molecules, Cytokines and Chemokines. It also includes BioLegend pathway posters, an antibody usage calculator, and a lab timer.

There is an extensive collection of apps for science on the mobile science page.

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15 mobile apps in Life Sciences

Last October when FierceBiotech IT rounded up the top apps in life sciences, the industry was just coming to terms with the potential of mobile devices. Now life science software providers are waking up to the fact that mobile is more than an opportunity, it is a necessity. It is increasingly hard to envisage a successful software company that lacks a mobile strategy.

Read more: 15 mobile apps in Life Sciences - 2012 - FierceBiotechIT

There is an extensive collection of apps for science on the mobile science page.

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TB Mobile app

The TB Mobile app presents over 700 small molecules structures screened versus Mtb and their targets. This data is only available in Collaborative Drug Discovery, Inc. (CDD). To which has been added published data on target, essentiality, links to literature (PubMed), genes (tbdb.org), pathways (TBCyc, which provides a pathway-based visualization of the entire cellular biochemical network) and human homolog information. The structures, names and miscellaneous data for these drugs are stored within the app, and made available for browsing. The drugs can be filtered, searched by name or structure, and viewed in 2D. There are several functions for making use of the data. The app therefore merges cheminformatics and bioinformatics information.

Now added to the mobile science page.

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SPRESImobile 2.0 now available: full reaction searching SPRESImobile 2.0 now available: full reaction searching

The SPRESImobile app provides access to InfoChem‘s SPRESI database. It runs on Apple iOS devices (iPhones, iPods and iPads) and is free on the iTunes AppStore. The latest version extends the search capabilities to include searching by reaction: various types of exact, substructure and similarity searches can be performed. Furthermore, it is now possible for existing customers of SPRESI to provide their user credentials within the app, which unlocks the entirety of the database content, rather than the default curated ChemReact subset that is made available to all.

More apps are on the mobile science page

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ChemDoodle mobile updated

ChemDoodle mobile has just been updated

ChemDoodle Mobile is a calculator for drawn organic structures. There are four main windows: Draw, Calculate, Spectra and Help. The Draw window shows a typical ChemDoodle sketcher, where you can draw and store your structures. The Calculate page calculates properties and the Spectra page simulates NMR spectra. All spectra are interactive. The Help page contains a detailed help guide.

Calculations 1. Molecular Formula 2. Molecular Mass 3. Monoisotopic Mass 4. Degree of Unsaturation 5. Hydrogen Bond Acceptors 6. Hydrogen Bond Donors 7. Average Molecular Polarizability 8. Molar Refractivity 9. Polar Surface Area 10. logP Spectra 1. Mass Parent Peak (Isotopic Distribution) 2. 1H NMR 3. 13C NMR

There are more apps on the mobile science page

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iOS and OS X Graphing Library

iOS and OS X Graphing Library Free For Development

VVI today announced the availability of it’s graphing library for iPhone, iPad, iPod touch and Macs. Version 10.8.3 of the graphing libraries and frameworks, aka Vvidget Code, brings the following achievements:

  • Supports deployment to OS X versions 10.6 to 10.8 (Macs) and iOS versions 4.3 to 5.1 (iPhone, iPad and iPod Touch).
  • Supports development on OS X versions 10.6 to 10.8 and Xcode 3.2 to 4.4.1.
  • Uses native API on deployment platforms for the fastest and most robust possible implementation. That is, Cocoa Touch for the iPhone, iPad and iPod Touch and Cocoa for the Mac.
  • Use for development is free.
  • Eleven Vvidget-based applications available from VVI on the iTunes App Store for iPhone, iPad and iPod Touch and on the Mac App Store demonstrate Vvidget Code in actual situations.
  • Applications based upon Vvidget Code are free-standing and require no additional installs. Vvidget Code itself can be installed using package installers or shared using free-standing Xcode projects.
  • Download and install instructions are at: Download And Install Vvidget Code

Please email sales@vvi.com for additional information.

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Latest Market Share Data

Net Applications have published the August data for Net market share. For the first time since Net Applications began collecting data the Mac share has topped 7% (7.13%), looking at the different versions of the Mac operating system 10.7 has 34%, 10.6 has 33% and 10.8 (Mountain Lion) has 20% after being available for barely a month.

In the mobile arena there has been little change over the last three months with iOS accounting for 66% and Android 21%, JavaME, Blackberry and Symbian continue to slowly decline.

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PyMOL now on iPad

Schrodinger have just announced the release of PyMOL on the iPad. It is a free download from the App Store. With the app you can:-

  • View 3D molecular structures, images, and PDFs
  • Search and download data from the PDB, PubChem, Dropbox, or your own custom server.
  • Intuitively interactive: rotate, pan, twist, zoom, center, and adjust clipping planes, with simple gestures
  • Select atoms, residues, molecules, chains, objects, etc. – just by tapping the screen
  • Easy-to-use visualization presets cover the majority of visualization needs such as bond representations and surfaces.
  • Distance calculations, structure alignments, anaglyph 3D, and much more

photo

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iSpartan and iSpartan server

I was wondering when someone would use an iPad as the front-end to a fully featured modelling package running on a remote server, looks like Wavefunction have done a pretty impressive job with taking their sophisticated Spartan computational chemistry package from the desktop to mobile devices.

iSpartan creates molecules as familiar 2D sketches, directly converts these into 3D structures, and calculates low energy conformations. Atomic and molecular properties, NMR and infrared spectra, molecular orbitals and electrostatic potential maps are available from a 5,000 molecule subset of the Spartan Spectra and Properties Database (SSPD). The database may also be searched by substructure. Properties, spectra and graphical models of molecules in the SSPD subset are available for examination.

iSpartan Server is an available add-on to the iSpartan app. iSpartan Server installs on a Windows or Macintosh computer and converts iSpartan from an application whose primary utility is sketching molecules in 2D and visualizing them in 3D, into an open-ended molecular modeling research tool providing access to the full Spartan Spectra and Properties Database (SSPD), currently ~170,000 molecules) and to the computational engines used to produce the data in the SSPD. For molecules not included in the database, connection to iSpartan Server supports calculation of structures, properties, and spectra for all user generated molecules from iSpartan running on the iPad, iPhone, and iPodTouch.

iSpartanServer

There is a listing of science apps for iOS here

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Elemental for iPad 1.0

Elemental is the Dotmatics chemistry sketch utility provided at no charge

What's New in Version 1.0

  • Copy image to Camera Roll
  • Copy Image to Clipboard
  • File association (tap and hold to load in Elemental)

There is a listing of science apps for iOS here and a comparison of drawing packages here.

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Chemicalize now supports iPad

To benefit from the display clarity of devices such as the New iPad, chemicalize.org’s chemical structure image generator (built using Marvin) now handles high DPI displays (Retina displays), that also includes iPhone 4 and most new Android devices. Orientation change and touch events like drag, tap and swipe are enabled now.

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Mobile Science Publication

A new paper has just been published Redefining Cheminformatics with Intuitive Collaborative Mobile App

The proliferation of mobile devices such as smartphones and tablet computers has recently been extended to include a growing ecosystem of increasingly sophisticated chemistry software packages, commonly known as apps. The capabilities that these apps can offer to the practicing chemist are approaching those of conventional desktop-based software, but apps tend to be focused on a relatively small range of tasks. To overcome this, chemistry apps must be able to seamlessly transfer data to other apps, and through the network to other devices, as well as to other platforms, such as desktops and servers, using documented file formats and protocols whenever possible. This article describes the development and state of the art with regard to chemistry-aware apps that make use of facile data interchange, and some of the scenarios in which these apps can be inserted into a chemical information workflow to increase productivity. A selection of contemporary apps is used to demonstrate their relevance to pharmaceutical research. Mobile apps represent a novel approach for delivery of cheminformatics tools to chemists and other scientists, and indications suggest that mobile devices represent a disruptive technology for drug discovery, as they have been to many other industries.

There is a listing of science apps for iOS here.

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ChemFormula added to mobile science page

ChemFormula is a molecular formula and weight calculator ideal for students and anyone else who needs to quickly translate arbitrarily complex formulas into empirical formulas with molecular weights. Written by chemists, it includes support for a large number of common chemical abbreviations, functional groups, and protecting groups.

chemformula

There is a listing of science apps for iOS here.

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Mac and iOS Market Share Trends

Net Applications provide a monthly snapshot of the usage market share for various operating systems and platforms and while it is difficult to draw any conclusions from month to month changes it is interesting to go back and look at the change over longer time periods occasionally.

The June 2012 Mac desktop share stands at 6.72%, in June 2011 it was 5.67%, in June 2010 5.28%, in June 2009 4.74%, and in June 2008 3.70% so in the 4 years of records the Mac desktop share has nearly doubled.

In 2009 with the first analysis of the mobile usage market distribution iOS accounted for nearly 40%, JavaME 36%, Symbian 15% with Android on 2% since then we have seen dramatic changes in the market share with iOS now accounting for over 65%, Android up to 20%, JavaME down to 10% and Symbian almost eliminated with less than 2%. Mobile devices now account for more than 8% of the browsing usage up from around 2% two years ago.

The iPad accounts for nearly 37% of the mobile browsing usage and the iPhone 27%.

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ODDT Publication

There is a paper describing ODDT Open Drug Discovery Teams app.

Investigators of rare and neglected diseases can access some of the latest research in the field, plus data about the disorders themselves, through a recently launched free app for Apple devices.

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Approved Drugs App

The Approved Drugs app, which came out on the iTunes AppStore just a few days ago, is about to get its first update, whenever v1.0.1 gets approved. The update deals with the loading performance that currently incurs a bit of a hit when the app first loads, and can overload older devices that have less memory (i.e. crash). The reason the loading time does/did take awhile is that the data for 1300 drugs with 2D & 3D structures, enumerated tautomers, and various other adjunct data uses up quite a bit of memory, and it needs to be randomly accessible. The XML datasheet format used to store the data is suitable for streaming, but not at all for accessing arbitrary data entries without loading the whole thing into memory. The solution is a little bit inconvenient: invent a custom format for the read-only data that is indexed, so the app can rapidly scan the contents, in any order, without having to parse it all first.

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WWDC 2012

Registered Apple Developers can now access over 100 session videos to get an in-depth look at the latest in iOS and OS X.

https://developer.apple.com/videos/wwdc/2012

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Beilstein Journals App

Beilstein Journals App is available free of charge for iOS. Use this app to read all articles of the two Open Access journals Beilstein Journal of Organic Chemistry and Beilstein Journal of Nanotechnology.

beilsteinappi

Have a look at the mobile science page for more science apps for the iPhone and iPad.

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iMolview 1.5 released

Molsoft has just released a new version of iMolview an app that lets you browse protein, DNA, and small molecules in 3D on the iPhone and iPad.

The key new features include:

  • support for high resolution retina display in iPad3
  • simultaneous display of multiple proteins and superposition
  • side-by-side stereo
  • new tools for measuring and displaying distances and angles
  • export fully interactive chemical spreadsheets from ICM-Chemist to the iPad

imolview

There is also a video of iMolview in action

Have a look at the mobile science page for more science apps for the iPhone and iPad.

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Approved Drugs app added to mobile science page

The Approved Drugs app contains over a thousand chemical structures and names of small molecule drugs approved by the US Food & Drug Administration (FDA). Structures and names can be browsed in a list, searched by name, filtered by structural features, and ranked by similarity to a user-drawn structure. The detail view allows viewing of a 3D conformation as well as tautomers. Structures can be exported in a variety of ways, e.g. email, twitter, clipboard

There is a listing of science apps for iOS here.

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ChemSpider mobile updated

ChemSpider Mobile v1.1.1 released

There is a listing of science apps for iOS here.

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iKinasePro Universal

iKinasePro is now a universal app running on all iOS devices. iKinasePro for iOS4 provides access into Eidogen-Sertanty's Kinase Knowledgebase (KKB) with fast and powerful substructure-, similarity-, and super-similarity searching capability. In addition, you can search the kinome by target name, by finger-drawn chemical structures, and/or tap through a vast array of ring structures to circumnavigate the Kinome from several different perspectives

There is a listing of science apps for iOS here.

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SPRESImobile added to mobile science page

SPRESImobile is an app for Apple iPod, iPhone and iPad mobile devices, developed in collaboration with Eidogen-Sertanty. It provides direct access to ChemReact, a subset of the SPRESI structure and reaction database, which contains more than 400,000 unique reaction types and the related references.

photo

There is a listing of science apps for iOS here.

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MMDS UI updated

One of the challenges of creating apps for mobile devices is making functionality available via the user interface and the limited real estate. The UI of the mobile molecular data sheet (MMDS) has been updated to addresses a minor but persistent inconvenience: previously, the main command bank had to be open in order to exit from any of the editor panels.

UI_change

There is a listing of mobile science apps here.

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MyGenome app for iPad

It has now been a couple of years since the human genome was first sequenced and we are now seeing companies offering personal genome sequencing. Illumina are now offering MyGenome an iPad app that allows you to explore a real human genome. In due course they hope to allow you to explore your own genome.

There is more information about the app here.

Now added to the mobile science page.

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Reagents added to mobile science apps

Reagents, This application details the structures and functions of >80 reagents encountered in typical introductory organic chemistry courses.

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Chem+ is a chemical reference for your iPad

Chem+ is a chemical reference for your iPad. Databases Include: * NIOSH Pocket Guide (NPG) * Immediately Dangerous to Life and Health (IDLH) * Toxicity (TOX) * the Emergency Response Guidebook (ERG)

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Elemental for iPad

Elemental from Dotmatics a Chemistry Sketch Utility

Elemental is the Dotmatics chemistry sketch utility provided at no charge within many Dotmatics products. Now provided as a FREE app on the iTunes store.

elemental

There is a list of mobile science apps here.

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Continued rise of mobile browsing

The latests marketshare data from NetApplications is available, and while there has been a small increase in the Mac desktop share over the year up to 6.53%, perhaps the more interesting feature is the steady rise of mobile browsing. Over the year there has been a 50% increase in the use of mobile devices (smartphones+tablets) from less than 5% to 7.3%. Much of this is driven by iOS which now accounts for 63% of the mobile market share.

Looking at the weblog for the Macinchem website the results are similar with iOS accounting for over 7% of the visitors, software vendors need to think about support for mobile platforms if they have not already.

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Siri voice control of cloud computing

In this screencast BioTeam shows how it can orchestrate an Accelrys Pipeline Pilot experiment running on a remote cloud (BT Compute) via Apple iOS Siri voice control.

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ODDT Released

Open Drug Discovery Teams (ODDT) is now available on the iTunes Store.

The idea behind ODDT is that there are many rare of neglected diseases that might benefit from collaborative efforts from scientists from multiple disciplines, ODDT is an application that supports informal interactions, provides a means to explore relevant information in a flipboard like interface in particular information tagged by other scientists with similar interests. The image below gives you an idea of the topics currently discussed.

oddt

This slideshow explains the genesis of the project, and how it has evolved.

So why not fire up iTunes and download the free app and get involved?

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Mobile Molecular Datasheet has been updated

The Mobile Molecular DataSheet (MMDS) has been updated. Two major usability enhancements:

(1) Additional tool banks on the left and right side of the sketcher provide simplified drawing tools that are more familiar to users of desktop chemical drawing software.

(2) A tooltip system provides tips, live demonstrations and links to documentation.

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SPRESImobile added

SPRESImobile provides direct access to ChemReact, a subset of the SPRESI structure and reaction database, which contains more than 400,000 unique reaction types and the related references. SPRESImobile allows searching by name and structure queries, exact, substructure and All-in-one (Flex) search. There is a list of iOS applications on the mobile science page.

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Brain Lab

I’ve just added Brain Lab to the list of mobile science applications Brain Lab is a brain cell simulator, currently it offers

  1. A passive integrate and fire model
  2. A full Hodgkin-Huxley model with sodium and potassium channels
  3. A Library to learn more about brain science

Brain Lab offers real scientific brain cell models that can be used by anyone, no matter if you are a student, a scientist, or someone who is just interested in brain science. To carry out your experiments, they have set up a Lab for you with all the necessary equipment. If you need to brush up your brain science knowledge or look up a specific technical term, you can go to your Library and read it up. 

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Net Applications Mac global market share

The latest data from Net Applications is in, Mac OS X is up to around 7% whilst Windows is now down to just below 92%.

iOS continues to dominate the mobile/tablet market (60%), with Android (19%) and Java ME (14%) being the only others in to double figures.

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Open Drug Discovery Teams iOS app alpha test

The Open Drug Discovery Teams (ODDT) project is a mobile app primarily intended as a research topic aggregator of open science data integrated from various sources on the internet. It exists to facilitate interdisciplinary teamwork and to relieve the user from data overload. Initial research topics include areas of chemistry and adjacent molecule-oriented biomedical sciences, with an emphasis on those which are most amenable to open research at present. The ODDT project uses a free mobile app for iOS-based devices (iPhone, iPod and iPad) as the hub. The app has a Flipboard-inspired interface, and serverside infrastructure for hosting data and value added services. The project is open to participation from anyone, and much of the content is derived from public sources but is amenable to commercial data input and they are now looking for alpha testers. One of the key components is a back-end server that is in charge of monitoring the appearance of tweets with certain hash tags (#tuberculosis, #malaria, #hivaids, #huntingtons, #sanfilipposyndrome and #greenchemistry).

There is a screencast here to give you an idea of the functionality.

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VVI Graph SDK

VVI® today announced the availability of Vvidget Code, its Graph SDK for iPhone, iPad and Mac, version 10.7.6, bringing the following improvements:

The features are extensive and shown by the Graph app on the iTunes and Mac App Store. All the graphs in those applications are now available in the new version. See the links: Graph for iPhone, iPad and iPod touch and Graph for Mac to install those applications and test the Vvidget Code Graph SDK.

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iOS Simulator

A great tip from Dan at Dotmatics, if you want to know how your website might look on an iPhone/iPad use the iOS Simulator in the developers tools.

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iOS:Chart

A chart & graph library for iOS and Mac OS X developers.

  • Fully native Objective-C library for direct, easy use in any iOS XCode project.
  • Several samples and demo projects to make integration and getting started a snap.
  • Over 50 powerful graph types, including bar, line, area, pie, scatter, bubble and waterfall.
  • An easy-to-use yet powerful object oriented API gives you full control over your charts with a minimum of effort.
  • Real 3D graphs with controls to zoom, pan, rotate and skew!
  • Adjust and control every element on every chart. Multiple Y-axis, depth effects, reference lines, scale controls and much more.
  • The full power of the PGSDK (charting library of choice for MicroStrategy, IBM/Cognos and many more) now for your mobile application!

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Added 3 apps to Mobile Science Page

iFormulas is a clean, simple, easy to use mathematical formula reference guide. Formulas : Algebra, Calculus, Chemistry, Geometry and Trigonometry. Over 380 formulas, definitions, laws, properties, etc.

MyCalculator is an innovative 2D and 3D graphing calculator featuring One Touch Graphing™ and an innovative memory system to store and recall answers. Just touch the answer bar to store numbers in multiple memory slots.

MathStudio, formerly SpaceTime, is the most comprehensive math app available for iPhone and iPad. Whether you need a simple calculator to do your finances or a replacement for your TI graphing calculator,

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MolPrime added to mobile science page

MolPrime is a chemical structure drawing tool based on the unique sketcher from the Mobile Molecular DataSheet

Added to the Mobile Science Page.

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Chirys Draw added to mobile science page

Chirys Draw is an innovative, best-in-class application for drawing publication-quality molecular structures and reactions. Designed from the ground up for the iPad, Chirys Draw takes advantage of unique multi-touch capabilities to make drawing molecular structures and reactions easy and accurate. Chirys™ Sketch is an innovative, best-in-class application for drawing publication-quality molecular structures and reactions. Designed and built from Chirys Draw, the iPad version, Chirys Sketch takes advantage of unique multi-touch capabilities to make drawing molecular structures easy and accurate.

There are many more applications on the mobile science page.

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Added CMol to mobile science page

CMol is a molecular viewer designed specifically for the iPad, iPhone and iPod touch, offering a more powerful system for displaying and understanding biological molecules than has yet been seen on any iOS device.

There are many more applications on the mobile science page.

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