This article presents an overview of the development of two basic software libraries for image manipulation and data visualization in cryo-EM: emcore and emvis.

The analysis of large structural databases reveals general features and relationships among proteins, providing useful insight. A different approach is required to characterize ubiquitous secondary-structure elements, where flexibility is essential in order to capture small local differences. The ALEPH software is optimized for the analysis and the extraction of small protein folds by relying on their geometry rather than on their sequence. The annotation of the structural variability of a given fold provides valuable information for fragment-based molecular-replacement methods, in which testing alternative model hypotheses can succeed in solving difficult structures when no homology models are available or are successful. ARCIMBOLDO_BORGES combines the use of composite secondary-structure elements as a search model with density modification and tracing to reveal the rest of the structure when both steps are successful. This phasing method relies on general fold libraries describing variations around a given pattern of β-sheets and helices extracted using ALEPH. The program introduces characteristic vectors defined from the main-chain atoms as a way to describe the geometrical properties of the structure. ALEPH encodes structural properties in a graph network, the exploration of which allows secondary-structure annotation, decomposition of a structure into small compact folds, generation of libraries of models representing a variation of a given fold and finally superposition of these folds onto a target structure. These functions are available through a graphical interface designed to interactively show the results of structure manipulation, annotation, fold decomposition, clustering and library generation. ALEPH can produce pictures of the graphs, structures and folds for publication purposes.

Image-processing software has always been an integral part of structure determination by cryogenic electron microscopy (cryo-EM). Recent advances in hardware and software are recognized as one of the key factors in the so-called cryo-EM resolution revolution. Increasing computational power has opened many possibilities to consider more demanding algorithms, which in turn allow more complex biological problems to be tackled. Moreover, data processing has become more accessible to many experimental groups, with computations that used to last for many days at supercomputing facilities now being performed in hours on personal workstations. All of these advances, together with the rapid expansion of the community, continue to pose challenges and new demands on the software-development side. In this article, the development of emcore and emvis, two basic software libraries for image manipulation and data visualization in cryo-EM, is presented. The main goal is to provide basic functionality organized in modular components that other developers can reuse to implement new algorithms or build graphical applications. An additional aim is to showcase the importance of following established practices in software engineering, with the hope that this could be a first step towards a more standardized way of developing and distributing software in the field.

To download the free e-book Best of Both Worlds: Museums, Libraries, and Archives in a Digital Age, by G. Wayne Clough, Secretary of the Smithsonian, […]

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Tucked away on the lower levels of the Smithsonian’s National Museum of Natural History and National Museum of American History are some of science’s most […]

The post Smithsonian Libraries’ rare texts include early superstars of science appeared first on Smithsonian Insider.

Washington, D.C. is a city of symbols. The rites, rituals, and places that define Washington capture the aspirations of our nation and its citizens. Just […]

The post Trusted Sources: Why Museums and Libraries Are More Relevant Than Ever appeared first on Smithsonian Insider.

Smithsonian Institution Libraries has recently acquired a rare first edition of Darwin's Geological Observations on the Volcanic Islands, Visited During the Voyage of the H.M.S. Beagle.

The post With 1844 first edition, Smithsonian Libraries completes its collection of Charles Darwin’s three-volume geology series appeared first on Smithsonian Insider.

The Smithsonian Libraries offer a vast amount of resources to the general public. This video gives you a peek into the amazing world of discovery […]

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Here are some of the many resources the Smithsonian Libraries have to offer for Exploration, Encounter, Exchange in History

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File photo: Lorne Street Elementary students had to grab books from a book bin after their library was closed during the recession.; Credit: Annie Gilbertson/KPCC

More than 200 Los Angeles Unified School District elementary school libraries have reopened in just two months, according to district officials.

Recession-era budget cuts had left many libraries without staffing. The cuts persisted even when the economy began to improve: a year ago half of the district's 650,000 students were still without a librarian or library aide.

Without library workers, state law prohibits students from browsing collections, pulling reference materials or checking out books. 

“We have been living without libraries and, no, we don’t want to because they are essential for academic achievement and learning for our students," said Mark Bobrosky, a librarian at Walter Reed Middle School.

School board member Monica Ratliff created a task force to recommend ways to expand libraries after KPCC reported that Lorne Street Elementary in Northridge had a library full of books collecting dust.

"This idea of equity — we are trying to make sure we don't have library deserts," Ratliff said at the board's curriculum, instruction and assessment committee meeting on Tuesday.

Even when the board committed funds for elementary school libraries, the district found it hard to fill openings. Library aides worked just three hours a day, five days a week.

Members of the task force suggested assigning library aides to two schools, doubling their hours and providing benefits.  Elementary school libraries began to quickly reopen. 

But while conditions have improved for elementary students, middle school libraries are still hard hit, with nearly 65 percent of their campus libraries shuttered.

Bobrosky said reopening the libraries is vital for L.A. Unified's success in implementing the Common Core state standards, which require research projects incorporating a variety of texts.

This content is from Southern California Public Radio. View the original story at SCPR.org.

Digital check-outs are becoming an increasingly popular option.

The digital age isn't making libraries obsolete; it's making them more important than ever.

From centuries-old temples to sleek modern masterpieces, libraries are some of humanity's most beautiful architectural accomplishments.

The Nordic nation gets bookish at the 2018 Venice Architecture Biennale with an exposition dubbed 'Mind-Building'

Many public library systems are eliminating late fees on materials because they see them as a form of social inequity.

Americans went to libraries more than the movies in 2019, according to a new Gallup poll.

Decades' worth of contents present an untapped opportunity for TV studios and legacy content owners.

Check out these 5 cool Python libraries that the author has come across during an NLP project, and which have made their life easier.

Also: Coronavirus COVID-19 Genome Analysis using Biopython; LSTM for time series prediction; A Concise Course in Statistical Inference: The Free eBook; Exploring the Impact of Geographic Information Systems

5 cool Python libraries for Data Science; NLP Recipes: Best Practices and Examples; Deep Learning: The Free eBook; Demystifying the AI Infrastructure Stack; and more.

Deep Learning is a branch of artificial intelligence and a subset of machine learning that focuses on networks capable of, usually, unsupervised learning from unstructured and other forms of data. It is also known as deep structured learning or differential programming. Architectures inspired by deep learning find use in a range of fields, such as...

The interoperability of proof assistants and the integration of their libraries is a highly valued but elusive goal in the field of theorem proving. As a preparatory step, in previous work, we translated the libraries of multiple proof assistants, specifically the ones of Coq, HOL Light, IMPS, Isabelle, Mizar, and PVS into a universal format: OMDoc/MMT.

Each translation presented tremendous theoretical, technical, and social challenges, some universal and some system-specific, some solvable and some still open. In this paper, we survey these challenges and compare and evaluate the solutions we chose.

We believe similar library translations will be an essential part of any future system interoperability solution and our experiences will prove valuable to others undertaking such efforts.

A library of macrocyclic compounds of the formula (I) where part (A) is a bivalent radical, a —(CH2)y— bivalent radical or a covalent bond;where part (B) is a bivalent radical, a —(CH2)z— bivalent radical, or a covalent bond;where part (C) is a bivalent radical, a —(CH2)t— bivalent radical, or a covalent bond; andwhere part (T) is a —Y-L-Z— radical wherein Y is CH2 or CO, Z is NH or O and L is a bivalent radical. These compounds are useful for carrying out screening assays or as intermediates for the synthesis of other compounds of pharmaceutical interest. A process for the preparation of these compounds in a combinatorial manner, is also disclosed.

Cinesamples has launched the World Series Week, offering a 40% discount on a collection of cultural instruments from around the world. World Series instruments are perfect for adding unique and transformative sounds to your scores. In the film composer repertoire, instrumentation is one of many tools that can transform a simple piece of music. At […]

The post Cinesamples launches World Series Week: Get 40% off sample libraries appeared first on rekkerd.org.

Prime Loops has announced another lockdown sale with 50% off on Rast Sound sample libraries for a limited time. The sale features libraries with a variety of ethnic instruments and vocals, including Kabak Kemane, Sufi Ney, Persian Vocal Samples, Inca Spirit Vocals, Sounds Of Morocco, Indian Flute, and lots more. Exclusive to Prime Loops, Rast […]

The post Prime Loops offers 50% OFF on Rast Sound sample libraries appeared first on rekkerd.org.

Five great websites that offer a variety of professional quality sample libraries and audio tools suited for any type of project or genre.

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The post 5 Websites That Offer Professional Quality Sample Libraries appeared first on Dubspot Blog.

Gov. Jay Inslee has released a four-phase plan to guide the reopening of Washington's economy and amenities. Here's an estimate of when things will start to open back up.

Gov. Jay Inslee has released a four-phase plan to guide the reopening of Washington's economy and amenities. Here's an estimate of when things will start to open back up.

Researchers are reporting an "alarming" loss in the number of qualified teacher librarians in schools, and they warn student literacy will continue to suffer if the trend is not reversed.

Submitted by Elaine Pritchard: Looking for some social interaction with your Libraries colleagues?  Join us for the next LibrariesConnect brown bag this Thursday, May 7, from noon – 12:30 p.m.  To join via Zoom:  https://osu.zoom.us/j/94746223336  Or call 1-301-715-8592, meeting ID 94746223336  LibrariesConnect brings our faculty and staff together in a relaxed environment where we can […]

Submitted by Casey Cramer: Now that we are living in a time with plenty of video conference calls – and are making these calls from our homes where pets, kids and significant others may appear in the background – we all have heard and seen some funny moments. What is the funniest Zoom moment you […]

Submitted by Nicole Hernandez: University Libraries participated in the RUSA Data in the Libraries webinar series this semester. The webinar recordings are now available online. The following webinar records are now available: Understanding and Working with APIs Data Processing and Visualization Open Data Data Basics and The Reference Interview Information on the webinar series, and […]

Submitted by Ashleigh Minor: Sign your team up today to participate in the University Libraries Zoom Pictionary May Madness Tournament!  Are you bummed you missed out on March Madness this year? Need a little break in the day to connect with colleagues and have some fun? We’re looking for teams of 4-6 players to challenge […]

From canceled author readings to lost revenue and visitors amid a government-ordered shutdown, bookstores and libraries are struggling to stay connected to their audiences during the coronavirus pandemic, which has closed most brick-and-mortar gathering spots indefinitely.

  Visiting libraries is great. Neat things to learn about communities, comfy places to sit, clean bathrooms. I went to...

It may be tempting at the start of a new project to create the first database tables manually, or write SQL scripts that you run manually, especially when you first have to spend a significant amount of time on sifting through all the migration libraries and then some more to get it working properly.

Going through this process did slow me down at the start of the project but I was determined to use a migration tool because hunting inexplicable bugs that only happen in production just to find out there is a definition mismatch between the production and development databases is not fun. Using such a tool also motivates you to write both the setup and teardown steps for each table while the current design is still fresh in your mind.

At first I considered a standalone migration tool because I expect them to be very good at that single task. However, learning the idiosyncrasies of a new tool and trying to make it fit seamlessly into my development workflow seemed like more trouble than it is worth.

I decided to stick with a Common Lisp library and found the following seven that work with PostgreSQL and/or Postmodern:

• Postmodern-passenger-pigeon
• database-migrations
• cl-migrations
• Mito
• Crane
• Orizuru-orm
• cl-mgr

I quickly discounted Crane and Mito because they are ORM (Object Relational Mapper) libraries which are way more complex than a dedicated migration library. Development on Crane have stalled some time ago and I don't feel it is mature enough for frictionless use yet. Mito declares itself as being in Alpha state; also not mature enough yet.

I only stumbled onto cl-mgr and Orizuru-orm long after making my decision so I did not investigate them seriously. Orizuru-orm is in any case an ORM which I would have discounted because it is too complex for my needs. CL-mgr looks simple, which is a good thing. It is based on cl-dbi which makes it a good candidate if you foresee switching databases but even if I discovered it sooner I would have discounted it for the same reason as CL-migrations.

CL-migrations looks very promising. It is a simple library focusing only on migrations. It uses clsql to interface with the database which bothered me because I already committed to using Postmodern and I try to avoid adding a lot of unused code to my projects. The positive side is that it interfaces to many different databases so it is a good candidate if you are not committed to using Postmodern. It is also a stable code base with no outstanding bug reports.

The two projects I focused on was Postmodern-passenger-pigeon and Database-migrations because they both use Postmodern for a database interface.

Postmodern-passenger-pigeon was in active development at the time and it seemed safer to use than Database-migrations because it can do dry runs, which is a very nice feature when you are upgrading your production database and face the possibility of losing data when things go awry. Unfortunately I could not get it working within a reasonable amount of time.

I finally settled on Database-migrations. It is a small code base, focused on one task, it is mature and it uses Postmodern so it does not pull in a whole new database interface into my project. There are however some less positive issues.

The first issue is a hindrance during development. Every time the migrations ASDF system (or the file containing it, as ASDF prefers that all systems be defined in a single file) is recompiled it adds all the defined migrations to the migrations list. Though each one will only be applied once to the DB it is still bothersome. One can then clear the list with (setf database-migrations::*migrations* nil) but then only newly modified migration files will be added. The solution then is to touch the .asd file after clearing the migrations list.

The second negative point is quite dangerous. The downgrade function takes a target version as parameter, with a default target of 0. This means that if you execute downgrade without specifying a target version you delete your whole database.

I am currently using Database-migrations and it works well for me. If for some reason I need to switch I will use cl-migrations.

Using Database-migrations

To address the danger of unintentionally deleting my database I created a wrapper function that does both upgrade and downgrade, and it requires a target version number.

Another practical issue I discovered is that upgrades and downgrades happen in the same order as they are defined in the migration file. If you create two tables in a single file where table 2 depends on table 1 then you can not revert / downgrade because Database-migrations will attempt to delete table 1 before table 2. The solution here is to use the def-queries-migration macro (instead of def-query-migration) which defines multiple queries simultaneously . If you get overwhelmed by a single definition that defines multiple tables the other option is to stick with one migration definition per file.

Lindsay K Pino
Apr 20, 2020; 0:P119.001913v1-mcp.P119.001913
Perspective

Data independent acquisition (DIA) is an attractive alternative to standard shotgun proteomics methods for quantitative experiments. However, most DIA methods require collecting exhaustive, sample-specific spectrum libraries with data dependent acquisition (DDA) to detect and quantify peptides. In addition to working with non-human samples, studies of splice junctions, sequence variants, or simply working with small sample yields can make developing DDA-based spectrum libraries impractical. Here we illustrate how to acquire, queue, and validate DIA data without spectrum libraries, and provide a workflow to efficiently generate DIA-only chromatogram libraries using gas-phase fractionation (GPF). We present best-practice methods for collecting DIA data using Orbitrap-based instruments, and develop an understanding for why DIA using an Orbitrap mass spectrometer should be approached differently than when using time-of-flight instruments. Finally, we discuss several methods for analyzing DIA data without libraries.

The November 2019 issue of College & Research Libraries is now freely available online. Visit the C&RL website for complete contents from 1939 to the present and follow C&RL on Facebook and Twitter for updates and discussion. Note: The November 2013 issue was the final print issue of College & Research Libraries. The journal began an online-only publication model in January 2014. [...]

The January 2020 issue of College & Research Libraries is now freely available online. Visit the C&RL website for complete contents from 1939 to the present and follow C&RL on Facebook and Twitter for updates and discussion. Note: The November 2013 issue was the final print issue of College & Research Libraries. The journal began an online-only publication model [...]

The March 2020 issue of College & Research Libraries is now freely available online. Visit the C&RL website for complete contents from 1939 to the present and followC&RL on Facebook and Twitter for updates and discussion. Note: The November 2013 issue was the final print issue of College & Research Libraries. The journal began an online-only publication model in [...]

The April 2020 special issue of College & Research Libraries, highlighting the projects of ACRL Academic Library Impact research grant recipients, is now freely available online. Visit the C&RL website for complete contents from 1939 to the present and followC&RL on Facebook and Twitter for updates and discussion. Note: The November 2013 issue was the [...]

The May 2020 issue of College & Research Libraries is now freely available online. Visit the C&RL website for complete contents from 1939 to the present and followC&RL on Facebook and Twitter for updates and discussion. Note: The November 2013 issue was the final print issue of College & Research Libraries. The journal began an online-only publication model [...]