Modelling Earth

 https://phys.org/news/2026-11-scientists-earth-simulation-life-planets.html

Increasing Scientific Productivity

https://phys.org/news/2025-05-fully-automated-tool-species-tree.amp

NASA Software Catalog

Among all these US restricted, US Government restricted, and publicly available software, there must be some hidden gems.  Look for them @  https://software.nasa.gov/

Require registration.

Small Step Towards Mind Control

         

I wonder how far we are from remote mind control; if signals can be recorded, they could be played back...

Wireless recording of neural activity with ultrasound Implanted devices that record neural activity in model organisms such as rats ideally should be as small as possible, remotely powered and able to transduce information wirelessly.

Seo et al. aim for all of these features by using neural dust to record from peripheral neurons in the mouse. Neural dust is a tiny recording system thI wonder how far we are from remote mind control; if signals can be recorded, they could be played back...

Wireless recording of neural activity with ultrasound Implanted devices that record neural activity in model organisms such as rats ideally should be as small as possible, remotely powered and able to transduce information wirelessly.

Seo et al. aim for all of these features by using neural dust to record from peripheral neurons in the mouse. Neural dust is a tiny recording system that consists mainly of electrodes and a piezoelectric crystal. The crystal reflects ultrasonic energy (sent from an external transducer) after neural activity picked up with the electrodes modulates the ultrasonic signal. Electrical activity can thus be inferred from the difference in emitted and received ultrasound signal. The researchers applied their technology in vivo to obtain electroneurographic and electromyographic recordings from rat sciatic nerve and skeletal muscles, respectively.

http://www.cell.com/neuron/pdf/S0896-6273(16)30344-0.pdf

REBOUND

REBOUND is a new multi-purpose N-body code which is freely available under an open-source license. It was designed for collisional dynamics such as planetary rings but can also solve the classical N-body problem.  It is described in a paper @ http://arxiv.org/pdf/1110.4876v2.pdf


Find it @ https://pypi.python.org/pypi/rebound/0.2.2

NetLogo

NetLogo is a multi-agent programmable modeling environment. It is used by tens of thousands of students, teachers and researchers worldwide. It also powers HubNet participatory simulations. It is authored by Uri Wilensky and developed at the CCL. You can download it free of charge.   Find it @ https://ccl.northwestern.edu/netlogo/ 


The book "An Introduction to Agent-Based Modeling: Modeling Natural, Social, and Engineered Complex Systems with NetLogo" provides an introduction to one of the primary methodologies for research in this new field of knowledge and uses NetLogo in its exercises.

Simulating Cells

This is a computer model of a bacterium which accounts for gene function and predicts unexpected emergent properties.  The paper may be found @ http://covertlab.stanford.edu/publicationpdfs/mgenitalium_whole_cell_2012_07_20.pdf

Software To Design Genes & Networks

"...many synthetic biologists ... are developing software of their own. Some programs make drawing up the plans for a new plasmid so effortless that high school students and untrained bio-hobbyists can do it. Others include simulators so researchers can predict how a new genetic circuit will work..."

Internet & Cloud for Astronomy

I really liked this paper since it uses software engineering and a species of (Internet/Cloud)-based services to render its results.

Look at page 3:

"We created a workflow, i.e. an automatic data retrieval and analysis system to search for cE galaxies in large data collections provided by the Virtual Observatory (VO, (12)). It comprised the following steps. (i) Identify nearby galaxy clusters at redshifts z < 0.055 using the Vizier Service (13) at the Centre de Donn´ees Astronomiques de Strasbourg. Without this condition our potential candidate cE galaxies would have been too faint for spectroscopic follow-up. (ii)

Once the sources were identified, gather more precise measurements using other VO services including the NASA/IPAC Extragalactic Database (NED, (14)). (iii) Use the IVOA Simple Image access Protocol to find and fetch the HST images of selected galaxy clusters from the Hubble Legacy Archive (HLA, (15)). (iv) For each image, run the SExtractor source identification software (16) to obtain half-light radii, total luminosities and approximate light profiles for all galaxies in each frame. (v) Apply color corrections to homogenize the results for all photometric bands and use the surface brightness – half-light radius criteria to find cE candidates. (vi) Finally, query NED, Vizier and a database of Sloan Digital Sky Survey Data Release 7 (17) to find additional information for candidate objects, such as published redshifts and integrated photometry."

A Population of Compact Elliptical Galaxies Detected with the Virtual Observatory

Genetic Algorithms & Einstein Equations

I think that genetic algorithms may be used to automatically discover new (exact and approximate) solutions of Einstein Equations. I have written a little bit on how to do so here @ https://skydrive.live.com/?sc=documents&cid=58aac97211c98e70#cid=58AAC97211C98E70&id=58AAC97211C98E70%21182

The Automation of Science

Ross D. King and his collaborators report the development of Robot Scientist "Adam," which has autonomously generated functional genomics hypotheses about the yeast Saccharomyces cerevisiae and experimentally tested these hypotheses by using laboratory automation. See: Science 3 April 2009: Vol. 324. no. 5923, pp. 85 - 89
and http://www.sciencemag.org/cgi/content/abstract/324/5923/85

A copy is available @ http://www.realscience.org.uk/Adamtherobotscientist.pdf

There is also this for Climate Science: http://www.blogger.com/post-edit.g?blogID=5337881532064470471&postID=2292395598974243071

Lattice QCD Software

Analysis of Open Source Software for Lattice Quantum Chromo Dynamics @ http://edoc.hu-berlin.de/master/grieger-jens-2007-07-18/PDF/grieger.pdf

Systems Biology Ontology

http://www.ebi.ac.uk/sbo/

Systems Biology Graphical Notation

Systems Biology Graphical Notation (SBGN) project is an effort to standardize the graphical notation used in maps of biochemical and cellular processes studied in systems biology. It consists of 3 languages: a Process Description language, an Entity Relationship language, and a Activity Flow language.

The main project page may be found @ http://sbgn.org/Main_Page

An Example Of Machine-Vision in Life Sciences

In the article titled "High-throughput ethomics in large groups of Drosophila" we read:

"We present a camera-based method for automatically quantifying the individual and social behaviors of fruit flies, Drosophila melanogaster, interacting in a planar arena..."

There is free supplementary material – including videos –available @

http://www.nature.com/nmeth/journal/v6/n6/suppinfo/nmeth.1328_S1.html

Free Chemical Drawing Package

Symyx is offering its Symyx Draw 3.1 chemical drawing application as a free download for those wishing to use it for academic and home use. Symyx Draw 3.1 enables you to draw and edit complex chemical structures and reactions with ease. Find it @ http://www.symyx.com/micro/getdraw/

Lilly Science Grid

Eli Lilly has made its Discovery IT platform, known internally as the Lilly Science Grid (LSG), open source.

LSG is a plug-in hosting and deployment framework that sits on top of Microsoft’s Composite Application Block. It is a rich client that requires .NET 2.0 or higher.

The framework simplifies the task of creating new plug-ins by providing a Visual Studio template from which developers can quickly learn and expand. Users can choose which applications and plug-ins to use within an integrated environment.

Find it @ http://sourceforge.net/projects/lsg

Mathematica & Sculpture

Various artists have been using Mathematica to produce artistic structures:

http://www.georgehart.com/sculpture/sculpture.html

and

http://www.bathsheba.com/

I clicked on the http://www.bathsheba.com/gallery/interp.html link and I noticed that the structures created by Mathematica are pleasing if they are the size of ornamental jewelry or house-hold goods; i.e. much smaller than the size of a human being.

But they do not "work" when their scale is large (comparable or larger than the size of a human being). They do not look pleasing as "stand-alone" sculptures for the most part; there is too much regularity and therefore they look boring since there is nothing beyond structure.

I am intrigued by this dependence of the sense of beauty on the scale of the work of art and the typical size of a human being.

It reminds me of what Protagoras is purported to have said in 485 B.C., "Man is the measure of everything."

Converting Protein Sequences Into Classical Music

UCLA molecular biologists Rie Takahashi and Jeffrey H. Miller have converted protein sequences into original classical music.





"We converted the sequence of proteins into music and can get an auditory signal for every protein," said Jeffrey H. Miller, distinguished professor of microbiology, immunology and molecular genetics, and a member of UCLA's Molecular Biology Institute. "Every protein will have its unique auditory signature because every protein has a unique sequence. You can hear the sequence of the protein."

"We assigned a chord to each amino acid," said Rie Takahashi, a UCLA research assistant and an award-winning, classically trained piano player. "We want to see if we can hear patterns within the music, as opposed to looking at the letters of an amino acid or protein sequence. We can listen to a protein, as opposed to just looking at it."

The building blocks of proteins are linear sequences of 20 different amino acids. Assigning one note for each amino acid therefore results in a 20-note scale.

"A 20-note scale is too large a range," Takahashi said. "You need a reduced scale, so we paired similar amino acids together and used chords and chord variations for each amino acid. We used each component of the music to indicate a specific characteristic of the protein. We are faithful in the conversion from the sequence to the music. The rhythm is dictated by the protein sequence."

You can listen to the compositions and even submit your own genetic sequence and have it transcribed @ http://www.mimg.ucla.edu/faculty/miller_jh/gene2music/examples.html