Quantum ESPRESSO

Quantum ESPRESSO is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.
Find Quantum ESPRESSO at: http://www.quantum-espresso.org/

Share
Posted in Condensed Matter | Leave a comment

Icy

Icy is an image analysis software primarily targeted at biological needs. It provides high-quality tools for biological image processing tasks, such as filtering (linear, nonlinear, morphological, etc.), cell segmentation, particles detection, tracking, multiple-class thresholding, measurements, microscope control, etc. It is designed to work on sequences from 2D to 5D (X, Y, Z, time, color channel), and runs on Windows, MacOS, Linux.
Find Icy at: http://icy.bioimageanalysis.org/

Share
Posted in Tools | Leave a comment

cadnano

Cadnano simplifies and enhances the process of designing three-dimensional DNA origami nanostructures. Through its user-friendly 2D and 3D interfaces it accelerates the creation of arbitrary designs. The embedded rules within Cadnano paired with the finite element analysis performed by cando, provide relative certainty of the stability of the structures.
Find cadnano at: http://cadnano.org/

Share
Posted in Nanotechnology | Leave a comment

Open Science consulting gig with the American Heart Association

I just got notification about a short-term consulting gig with the American Heart Association that is specifically related to issues of Open Science:

The American Heart Association has recently formed a task to explore and determine AHA’s role in open science.  Our specific interest at this time is focused on data repositories for finalized research data.  We are currently looking for a consultant to assist in gathering background information for this task force in the following areas:

  • What open science is, and how it relates to the AHA.  This should be approached more broadly than just our data focus so the committee is aware of other research transparency opportunities.
  • What other similar organizations are doing relative to open science and making data and publications available (e.g. NIH, HHMI, ACS, EU, etc.) The AHA can provide contact information within most these organizations.  We would like to see comparisons to about 6 similar organizations.  Our publishing area has looked at policies related to public access to publications, but this task force will be looking at how open access could impact our research program.
  • Existing repositories in use which can hold the types of data that AHA funded grants produce.
  • Legal, data design, or intellectual property issues with requiring researchers to store their data in a repository.
  • Documenting issues that should be addressed by the task force if they decide to move forward (e.g. timing for providing data, retention of data, definition of data to store, requiring common terminology, issues related to the re-use of the stored data etc.)

We anticipate that these efforts may involve the consultant 5-10 hours a week for a 6 week time period.   The project will begin in mid-October and would ideally be completed by Dec 1st.  Consultants that are interested in this project should provide a summary of their qualifications by October 12th.

 

Belinda Orland

Research Information Manager

Division of Research Administration

 

American Heart Association/American Stroke Association 

7272 Greenville Avenue
Dallas, TX 75231
214 360 6110
belinda.orland@heart.org

Share
Posted in Uncategorized | Leave a comment

Advice to junior faculty who want to do get promoted doing Open Science

I recently sent some advice to a colleague who is coming up for tenure at another university.  He’s quite well known in the Open Science community and is trying to figure out how best to make the case to his tenure committee that the open science contributions he has made in addition to his traditional journal publications are important.  We’re talking some major contributions here — lab protocols on OpenWetWare, open lecture materials on slideshare, data files released with CC0, videos of lab protocols on Benchfly, and he’s a regular contributor to science discussions on FriendFeed.

The advice I gave him was basically to make the committee’s job of measuring these contributions easier.  Here’s the advice (in a slightly edited form):

The audience for most tenure documents (and particularly the external letters) is a committee of non-specialists that advises the provost or other high-ranking administrator.  These committees are often somewhat skeptical of departments and candidates and are looking for external validation of what they are reading in the tenure dossier and the packet prepared by the departments.  They are swayed by real experts in the field (named chairs at other institutions, national academy members, people at top 10 institutions) and by things they can measure (publications, h-indices, grant money, citation counts). If you want to add a non-traditional contribution to a tenure dossier, you should also include a way of measuring the importance of that contribution.

First, if the rules of your institution allow it, make sure there is a strong defense of open ways of doing science in your dossier (1-2 paragraphs or so).  Make the case that it is important to consider non-standard contributions even though previous tenure committees did not.

Use as many metrics to back up your contributions as you can. Make a case that each of your software releases counts as much as a full publication, and use download statistics as if they were directly comparable to academic citations.  List external users of your software as if they were research collaborators, because they are!  If you can collect them, include download statistics on open contributions to sites like OpenWetware and Wikipedia.

If your institution’s rules allow it, make sections directly under your publications for  “Published Datasets”, “Contributed Software”, “Published Protocols & Notebooks”, “Scientific Videos”.  In each section, list authors, a title, description, and URL of the resource you have contributed along with a count of downloads or views, and a list of other groups using your data. Make this look as much like your publication section as possible, as you can then make the argument that these things should be treated with a similar weight to traditional academic publication.   Provide the metrics in the document so that your committees aren’t guessing about how important something is.  I can’t emphasize this enough – citation counts are easy for a committee to dig up – download stats are harder.  Do the measurement work for your committee and they’ll make the assumption that your metrics are important.

So that’s the advice.  I’ve been involved in a few internal tenure discussions, and the metrics are always important.  If there isn’t an easy analogy to something in my own experience, I look to the candidate’s documents and the external letters to tell me why something matters.

Share
Posted in open science, Science | Leave a comment

An informal definition of OpenScience

Over at the open-science mailing list at okfn.org, Michael Nielsen just posted a great “informal” definition of open science:

 

Open science is the idea that scientific knowledge of all kinds should be openly shared as early as is practical in the discovery process.

The discussion on the list has been very interesting, but that particular “informal” definition is great because it gets at why we’re struggling with established social norms in science given the new technological methods of communicating results:

 

…when the journal system was developed in the 17th and 18th centuries it was an excellent example of open science.  The journals are perhaps the most open system for the dissemination of knowledge that can be constructed — if you’re working with 17th century technology.  But, of course, today we can do a lot better.

Share
Posted in open science, Science | Tagged , | 9 Comments

Puma-EM

Puma-EM is a code that allows the computation of various electromagnetic quantities when a target is excited by an electromagnetic source. These quantities are the scattered fields and the currents on the surface of the target. It can compute: monostatic RCS for a variety of angles or positions (SAR) bistatic RCS for a variety of angles Antenna pattern electric and/or magnetic dipole excitation plane-wave excitation a combination of the above
Find Puma-EM at: http://puma-em.sourceforge.net/index.html

Share
Posted in Physics | Leave a comment

Maxima

Maxima is a system for the manipulation of symbolic and numerical expressions, including differentiation, integration, Taylor series, Laplace transforms, ordinary differential equations, systems of linear equations, polynomials, and sets, lists, vectors, matrices, and tensors. Maxima yields high precision numeric results by using exact fractions, arbitrary precision integers, and variable precision floating point numbers. Maxima can plot functions and data in two and three dimensions. Also has a graphical interface built in wxWidgets called wxMaxima (http://andrejv.github.com/wxmaxima/).
Find Maxima at: http://maxima.sourceforge.net/

Share
Posted in Mathematics | Leave a comment

Finite Element Method Magnetics – FEMM

FEMMis a suite of programs for solving lowfrequency electromagnetic problems on two-dimensional planar and axisymmetric domains. The program currently addresses linear/nonlinear magnetostatic problems, linear/nonlinear time harmonic magnetic problems, linear electrostatic problems, and steady-state heat flow problems.
Find Finite Element Method Magnetics – FEMM at: http://www.femm.info/wiki/HomePage

Share
Posted in Magnetism | Leave a comment

MPB

The MIT Photonic-Bands (MPB) package is a free program for computing the band structures (dispersion relations) and electromagnetic modes of periodic dielectric structures, on both serial and parallel computers. It was developed by Steven G. Johnson at MIT along with the Joannopoulos Ab Initio Physics group.
Find MPB at: http://ab-initio.mit.edu/wiki/index.php/MIT_Photonic_Bands

Share
Posted in Optics | Leave a comment