User:Jarle Pahr/Applications

Interesting online and mobile/tablet applications:

http://genengnews.com/insight-and-intelligence/the-best-science-apps/77899849/

)Portals=

http://www.appbrain.com/

Mobile/tablet apps

http://www.zappylab.com/

iPad

https://itunes.apple.com/app/biogene/id333180084?mt=8

http://research.oicr.on.ca/genomepad/

http://libraries.umdnj.edu/toolkits/Bioinformatics/mobile.html

Illumina MyGenome: https://itunes.apple.com/us/app/mygenome/id516405838?mt=8

Android

http://www.androidfreeware.net/download-bioinformatics-info.html

SimGene: http://www.appbrain.com/app/simgene/com.japanbioinformatics.simgene

SimAlign: http://www.appbrain.com/app/simalign/com.japanbioinformatics.simalign

http://edwards.sdsu.edu/labsite/index.php/josh/105-genomesearch-demo-online

http://biogenie.sourceforge.net/

http://en.wikipedia.org/wiki/List_of_open_source_Android_applications

Colony counters:

http://promega.wordpress.com/2013/03/29/now-available-for-purchase-promega-colony-counter-app/

http://www.appbrain.com/app/colony-counter-%28-automated-%29/air.com.bfrontier.flex.ColonyCounterPro

http://www.thebioblog.com/apps-for-scientists-promega-colony-counter/

http://biologigaragen.org/?p=122

https://groups.google.com/forum/?fromgroups=#!topic/biologigaragen/jAkAI81PI4Y

http://www.colonycount.org/

Programming

General

Which language should you build your app in? http://mashable.com/2012/07/11/language-app/

Corona SDK: http://ipad.about.com/od/iPad-App-Dev/fr/Review-Corona-SDK-For-iPhone-And-iPad-Development.htm

Codea: http://ipad.appstorm.net/roundups/developer/codea-lua-programming-on-your-ipad/

http://en.wikipedia.org/wiki/Mobile_application_development

Eclipse

How-to's:

Open a project:

Select Window -> Show view -> Package explorer.

Select project / application in Package explorer tab.

http://www.programmingodyssey.com/2011/12/running-android-sample-projects-from.html

Android

MIT AppInventor

Tutorials: http://appinventor.mit.edu/explore/tutorials.html

Concepts

• Activity:
• AndroidManifest.xml: A file declaring various properties of an application. All activities and services of the application must be declared in AndroidManifest.xml. The file also declares the required permission for the program.

• Intent: an object that provides runtime binding between separate components (such as two activities). See http://developer.android.com/reference/android/content/Intent.html Most often used to start another activity.

• Resources: Resource files like images can be kept separate from the source code, and are stored in a res/ folder. Individual resources can be accessed using the Resources class. Every resource has a corresponding resource object in the project's gen/R.java file. The R.java file is generated by the SDK when the app is compiled.

• Resource object: A unique integer name associated with an app resource (for example a bitmap, layout file or string). See http://developer.android.com/training/basics/firstapp/building-ui.html

• ADV: Android Virtual Device.

• ADB: Android Debug Bride. Command line tool that facilitates communication between Ecclipse and Android device (physical or virtual). Invoked by DDMS. See http://developer.android.com/tools/help/adb.html Can be used to install an application with the command adb install <path_to_apk> To see connected devises, enter "adb devices" in the directory sdk\platform-tools. Packages can be uninstalled with the uninstall command: adb uninstall <apk_name>

• DDMS: Dalvik Debug Monitor Server.

• View object: Usually a UI element like a button or text field.

• viewGroup: Invisible containers for view objects which define their layout.

Android specific methods and functions

intent.putExtra(key,value): Adds a key-value pair as an "extra" key-value pair to the intent.

startActivity (Intent, options): Start a new activity.

getIntent() : Returns the intent that started the activity.

How-tos

http://stackoverflow.com/questions/4992357/how-to-load-my-app-from-eclipse-to-my-android-phone-instead-of-avd

http://jamesgiang.wordpress.com/2010/04/25/adb-drivers-for-htc-desire/

http://www.edumobile.org/android/android-tutorial/what-is-ddms-and-how-it-works/

http://developer.android.com/guide/faq/commontasks.html

http://developer.android.com/tools/building/building-eclipse.html

http://developer.android.com/tools/building/index.html

Layout:

http://developer.android.com/guide/topics/ui/declaring-layout.html

Layout can be declared in xml, or in code by creating and manipulating view objects.

Text fields:

http://developer.android.com/guide/topics/ui/controls/text.html

Trouble-shooting

http://stackoverflow.com/questions/5118713/eclipse-gets-stuck-when-trying-to-launch-android-app

Links

http://androidresearch.wordpress.com/

http://www.herongyang.com/Android/

http://developer.android.com/training/basics/firstapp/creating-project.html

http://www.xda-developers.com/android/want-to-learn-how-to-program-for-android-start-here/

http://answers.oreilly.com/topic/1133-how-to-start-programming-in-android/

http://www.coreservlets.com/android-tutorial/

http://www.codeproject.com/Articles/102065/Android-A-beginner-s-guide

http://forum.xda-developers.com/showthread.php?p=7395098

http://en.wikipedia.org/wiki/Android_software_development

http://en.wikipedia.org/wiki/Android_%28operating_system%29

http://androidforums.com/android-applications/

http://www.anddev.org/

http://en.wikipedia.org/wiki/Google_App_Inventor

http://appinventor.mit.edu/

Android Development Tutorial Based on Android 4.2: http://www.vogella.com/articles/Android/article.html

Solutions for common Android development problems: http://www.vogella.com/articles/AndroidDevelopmentProblems/article.html

http://developer.android.com/tools/device.html

https://sites.google.com/a/android.com/tools/

http://en.wikipedia.org/wiki/CyanogenMod

http://en.wikipedia.org/wiki/Replicant_%28operating_system%29

Ideas

Simple:

• Ligation mix calculator.
• pH adjustment volume calculator
• Pipette operation planner. Determine the most practical/"optimal" way to perform pipetting operations, given specified objectives (volume accuracy, concentration accuracy, minimize waste).

Intermediate:

• Twitter filter. List twitter users fulfilling certain criteria, such as having certain keyword in their description (f.ex., "bioinforamatics"), follower/following ratio, etc.
• Twitterati. Network analysis and display of data from Twitter. For an inspiration, see https://nodexlgraphgallery.org/Pages/Graph.aspx?graphID=5717
• Bibliographer. Given a citation database, visualize a citation network.
• Backtracker: For a webpage selected from browsing history, show how you ended up there.
• Speciator: Group sequences by average nucleotide identity. Will the grouping agree with existing species classifications? See http://www.biomedcentral.com/1471-2180/12/302

Complex:

• ResourcePlanner: Set project priorities and allocate time use.
• Article scraper: Fetch articles that are linked to in a Twitter feed or appear in other data streams (recent.ly, etc.)
• JobGuide: Gather and present job postings from several job portals.

• Lab wizard. "Evidence based (= rational) lab management"? Estimate probabilities of success based on emperical data or user-entered estimates (ex: What is the likelyhood that a given reaction will succeed?), and calculate the most rational work plan, taking into account the estimated time use for each operation.

For example: If one procedure takes 10 min and has 60 % chance of success, and another takes 3 h and has 90 % of success, both yielding the same product, what procedure should be chosen? Depending on number of samples to be processed?

Elements which must be defined:

Operations: Time use, probability of success. Necessary materials.

Sample types:

• Sample tracker (barcodes?)

A scrollable lab chart/tree, showing relationship of samples, experiment and results.

Example: Far left, start with initial sample(s)/material(s) as root(s) of the tree(s). As work progresses the tree/graph branches out (one sample used several times) and re-combines (several samples used in one operation). Chart must be scrollable both horizontally (time) and vertically (to allow for many samples tree)

Horizontal line would show at least date/time. Could also incorporate milestones and events. Elements in the tree should be collapsable for easier viewing. Could also consider showing planned operations. (integrate with a "lab wizard"?)

• Data clustering and visualization agent.

Query a database of experiments with associated data, and perform visualization and clustering of experiments/data. For example, show all experiments that used medium X. Compare data of type Y (example, growth rate) between experiments using mediums A and B. Rank experimental conditions by the value of one output (for example, which growth medium gave highest growth rate)? For a heterogenous collection of experiments, cluster experiments by similarity in conditions (criteria for clustering/computing distance must be decided).

A sequence result evaluator? :

• Estimate average error rates for sequencing results.
• Based on above, define null hypothesis as "Real sequence is identical to the theoretical sequence", and use sequencing data to attempt to refute the null hypothesis. Use basecall quality values to estimate the probability that any given base is wrong.

Cloning plan helper:

Verification "wizard": Input: Plasmid sequence, region of plasmid considered insert, available restriction enzymes. Output: Suggested restriction digest for verifying insert (taking into account minimum fragment length to achieve visualization on gel).