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 […]

Feb 2020 article "...Wright, Bradfield, & Cairns (2013) noted a methodological separation of the intuitive logics approach popularized by Royal Dutch Shell (Wack, 1985a, 1985b) from firm‐level strategy concepts like business models (Zott, Amit, & Massa, 2011), competitive positioning (Porter, 1985), and resource capabilities (Barney, 1991)... The weakening of the connection, related to both the use of scenario planning and the research into it, is the historical connection to strategy process research."

NY-Vocalist, Benita Charles Will Be The Featured Artist For The Concert & Speaker Series At The Harlem Public Library On Oct 5th.

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.

Been thinking about this blog and how a lot of the work I’ve been doing lately doesn’t always lend itself...

  From a Vermont librarian: VPNs are really important and I’d like to remind our patrons about them, but it...

  I am looking for someone who can help me find and clear out excess data on one of my...

From a friend: Please explain to me your enthusiasm for controlled digital lending. Please let me know what you think...

Subtitled: What’s the Yahoo! Internet Life for this generation? From a friend: A nice older lady asked for advice on...

I was wondering if you might give my little women’s (boomers) some guidance as to a beginning graphic novel for...

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

I’ve been spending some of the wintertime outlasting the blues and making sure that Wikipedia’s got entries for every state...

It’s been an odd set of months. I got busy with Drop-In Time and then very un-busy. I’ve been keeping...

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.

In the Indonesian city of Semarang, international architecture firm SHAU has completed Microlibrary Warak Kayu, an inspiring new public space that raises the bar for community design and sustainable architecture. Prefabricated with only FSC-certified timber, the new neighborhood icon is the fifth built project in the Microlibrary series, an initiative to encourage reading in low-income areas by creating "socially performative multifunctional community spaces with environmentally conscious designs and materials." In addition to the exclusive use of sustainably grown and logged timbers, the project is the first library in Indonesia made entirely of FSC-certified wood. The Microlibrary Warak Kayu is also[...]

Toronto-based architecture firm RDHA has completed the Springdale Library and Komagata Maru Park, a new inclusive gathering space for Brampton, a city located about 45 minutes west of Toronto. Designed as a visual contrast to the flat suburban environment, the architects created an undulating landscape of hills that is reinforced by the building’s mountainous form. Surrounded by walls of glass and solar shades, the green-roofed library is powered by geothermal energy and is expected to achieve LEED Gold certification.[...]

The book that Duchess Meghan read to her son in Wednesday’s viral video was a gift from the media maven, who attended the Sussexes’ wedding back in 2018.

With libraries closed, L.A. librarians now work from home to help people find free ebooks, music and movies during the coronavirus crisis.

The goal is to provide financial services to billions of people around the world, including those who lack access to banking.

Fans of the Disney animated movie celebrated its addition to the National Film Registry.

oscon: Beginner's Guide to Computer Vision - 2D/3D image fundamentals, OpenCV, OpenNI Library + more http://t.co/ph2dKrC9W4 #oscon #tutorial

8 January 2020 , Volume 96, Number 1

8 January 2020 , Volume 96, Number 1

VOLUME 295 (2020) PAGES 3285–3300An incorrect graph was used in Fig. 5C. This error has now been corrected. Additionally, some of the statistics reported in the legend and text referring to Fig. 5C were incorrect. The F statistics for Fig. 5C should state Fken(3,16) = 7.454, p < 0.01; FCCCP(1,16) = 102.9, p < 0.0001; Finteraction(3,16) = 7.480, p < 0.01. This correction does not affect the results or conclusions of this work.jbc;295/17/5835/F5F1F5Figure 5C.

Qingbo Shu
Apr 1, 2020; 19:672-689
Research

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

Large-scale identification of N-linked intact glycopeptides by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) in human serum is challenging because of the wide dynamic range of serum protein abundances, the lack of a complete serum N-glycan database and the existence of proteoforms. In this regard, a spectral library search method was presented for the identification of N-linked intact glycopeptides from N-linked glycoproteins in human serum with target-decoy and motif-specific false discovery rate (FDR) control. Serum proteins were firstly separated into low-abundance and high-abundance proteins by acetonitrile (ACN) precipitation. After digestion, the N-linked intact glycopeptides were enriched by hydrophilic interaction liquid chromatography (HILIC) and a portion of the enriched N-linked intact glycopeptides were processed by Peptide-N-Glycosidase F (PNGase F) to generate N-linked deglycopeptides. Both N-linked intact glycopeptides and deglycopeptides were analyzed by LC-MS/MS. From N-linked deglycopeptides data sets, 764 N-linked glycoproteins, 1699 N-linked glycosites and 3328 unique N-linked deglycopeptides were identified. Four types of N-linked glycosylation motifs (NXS/T/C/V, X=P) were used to recognize the N-linked deglycopeptides. The spectra of these N-linked deglycopeptides were utilized for N-linked deglycopeptides library construction and identification of N-linked intact glycopeptides. A database containing 739 N-glycan masses was constructed and utilized during spectral library search for the identification of N-linked intact glycopeptides. In total, 526 N-linked glycoproteins, 1036 N-linked glycosites, 22,677 N-linked intact glycopeptides and 738 N-glycan masses were identified under 1% FDR, representing the most in-depth serum N-glycoproteome identified by LC-MS/MS at N-linked intact glycopeptide level.

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.

VOLUME 295 (2020) PAGES 3285–3300An incorrect graph was used in Fig. 5C. This error has now been corrected. Additionally, some of the statistics reported in the legend and text referring to Fig. 5C were incorrect. The F statistics for Fig. 5C should state Fken(3,16) = 7.454, p < 0.01; FCCCP(1,16) = 102.9, p < 0.0001; Finteraction(3,16) = 7.480, p < 0.01. This correction does not affect the results or conclusions of this work.jbc;295/17/5835/F5F1F5Figure 5C.

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 [...]

Libraries.

Libraries -- Philosophy.

Data libraries.

Libraries -- Marketing.

Libraries -- Syria -- Dārayyā (Damascus)