Author Archives: Melissa Cox Norris

BioCyc Microbial Genomes and Metabolic Pathways Web Portal

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BioCyc Database Collection Logo

 

 

 

The BioCyc Microbial Genomes and Metabolic Pathways Web Portal is coming to the University of Cincinnati.

Beginning August 31st, researchers can access the full suite of databases in the BioCyc Database Collection. The BioCyc web portal from SRI International contains genome and metabolic-pathway information for over 10,000 microbes. BioCyc encyclopedias are unique in integrating a diverse range of data and providing a high level of curation for important microbes. BioCyc Pathway/Genome Databases (PGDB) describe the genome of an organism, as well as its biochemical pathways and (for a small fraction of organisms) its regulatory network. BioCyc bioinformatics tools combine unparalleled breadth and user friendliness and include a unique set of visualization tools to speed comprehension of its extensive and complex data.

BioCyc databases integrate extensive data for each organism, and provide platforms for analysis of large-scale datasets. BioCyc enables scientists to pursue several use cases:

  • BioCyc is a massive encyclopedic reference on microbial genes, metabolites, and pathways that integrates information from many sources. Scientists consult BioCyc to save large amounts of time finding, understanding, and synthesizing material from the primary literature.
  • BioCyc is a genome informatics and comparative genomics platform.
  • BioCyc enables exploration of a vast set of biological networks.
  • BioCyc provides gene-expression, metabolomics, and multi-omics analysis tools.
  • BioCyc provides executable metabolic models for a small but growing set of organisms.

BioCyc Informatics Tools

  • Search for genomes by name, taxonomy, phenotypic properties.
  • Gene information page
    • Retrieve amino-acid sequence and nucleotide sequence of arbitrary genome region.
    • Query genes by gene name, accession number, sequence length, replicon position, protein properties (pI, MW, protein features, subcellular location, ligand), GO terms.
  • Transcription-unit information page.
  • Genome Browser depicts genomic regions at user-selected resolution with semantic zooming that reveals new features at higher resolutions. Visible features include pseudogenes, promoters, transcription-factor binding sites, repeats, terminators, nucleotide sequence. Zoom to sequence. Generate genome poster.
  • BLAST search sequence-pattern search via patmatchMap SNPs to genes and show effects on translation.

Access this URL for more information about BioCyc databases and features: https://biocyc.org/intro.shtml.

Some additional links that may be helpful:

Webinars: https://biocyc.org/webinar.shtml

Guided tour: https://biocyc.org/samples.shtml

User guide: https://biocyc.org/PToolsWebsiteHowto.shtml

Data Sheet: BioCyc data sheet

Questions?

Contact:

Tiffany J. Grant, PhD
Interim, Assistant Director for Research and Informatics
Research Informationist
Co-Leader, Research Services
Health Sciences Library
Office: (513) 558-9153
E-mail: joffritm@ucmail.uc.edu
Web: http://libraries.uc.edu/digital-scholarship/data-services.html

Join UC Libraries for “The Great American Read” and Vote for Your Favorite Novel

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The Color Purple, Harry Potter, Gone Girl – is one of these your favorite novel? Did you enjoy or struggle reading The Grapes of Wrath, War and Peace or Heart of Darkness when assigned for class? Did you sneak read The Stand or Twilight when your teacher wasn’t looking? These favorite, or not-so-favorite, books are amongst the 100 best-loved novels up for consideration as “The Great American Read.”

The University of Cincinnati Libraries and CET are partnering to host three screenings of “The Great American Read,” 8-9 p.m., Tuesdays, Sept. 11 and 25 and Oct. 9 in the Digital Commons Space on the fourth floor of the Walter C. Langsam Library. The PBS series features some of the 100 best-loved novels with testimonials from celebrities, authors, notable Americans and book lovers across the country talking about their pick for “The Great American Read.” Fresh popcorn and refreshments will be served.

The themes of the three screenings will include:

  • Sept. 11 – The Great American Read Fall Kick-Off
    Join host Meredith Vieira in the search for America’s best-loved novel.
  • Sept. 25 – Heroes
    Take a journey with some literary heroes to examine what makes them complex and relatable.
  • Oct. 9 – What We Do For love
    Fall in love all over again with some of literature’s most beautiful romances.

 

RSVPs not required, but attendees are encouraged to mark “going” on the Facebook event: https://www.facebook.com/events/298457014220539/.

Can’t join us for the screenings? Visit “The Great American Read” at http://www.pbs.org/the-great-american-read/home/ to learn more and vote for your favorite novel.

Dean’s Corner: Welcome Back UC!

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I am currently visiting Kuala Lumpur, Malaysia for the International Federation of Library Associations and Institutions (IFLA) World Library and Information Congress along with some of my colleagues from UC Libraries, but I’m excited to return to UC and greet our new and returning students and faculty.

At IFLA’s World Conference with Library Chief Technology Officer May Chang and Global Services Librarian Hong Cheng. Behind us is Kuala Lumpur’s famous Petronas Towers.

Before we dive into the fall semester, here’s a brief overview of the last few months at UC Libraries.

Several key library positions were filled over the summer, including: associate director of business affairs Jeremy Berberich; business and data analytics librarian Maggie Patel; associate dean of library services Brad Warren; and content analyst Dorcas Washington. The Digital Scholarship Center also continued to grow, welcoming digital scholarship library fellow Erin McCabe and data visualization developer Ezra Edgerton. They joined software developer Zhaowei Ren, with the support of a grant from the Andrew W. Mellon Foundation.

UC Libraries joined HathiTrust, a national and international partnership of research institutions and libraries.

The Winkler Center Advisory Board hosted the annual Cecil Striker Society Lecture, “Cincinnati Children’s Hospital Impacting the Health of Children in Our Community and the World: The Past, Present and Future,” with co-lecturers Michael K. Farrell, MD and Bea Katz, PhD.

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Join Us for the 2018 Books by the Banks Poster Launch Featuring Artist Courttney Cooper

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books by the banks poster launchUC Libraries is an organizing partner of Books by the Banks: Cincinnati Regional Book Festival. Join us for the 2018 Poster Launch on Thursday, Sept. 13 from 5-7pm at the Visionaries + Voices’ Visionarium at 3054 Madison Road in Oakley.

This year, Books by the Banks collaborated with Visionaries + Voices and artist Courttney Cooper on the creation of the poster art (a snippet of which is included on the invite at the top of this page). The launch will include refreshments, introductions by V+V and Books by the Banks, the poster reveal, and then remarks and a short Q&A with Courttney Cooper. Copies of the 2018 poster will be available for sale at the launch.

Courttney Cooper creates intensely detailed maps from his physical and psychological experiences in Cincinnati, Ohio. Using everyday materials of a Bic pen and re-purposed paper, Courttney methodically pieces fragments of his life experiences together. Established in 2003, Visionaries + Voices is a non-profit organization that provides exhibition opportunities, studio space, supplies and support to more than 125 visual artists with disabilities. V+V artists actively contribute to the greater arts community through creative, educational and strategic partnerships with local and regional artists, schools and business leaders. For more on Courttney Cooper and Visionaries + Voices, visit https://visionariesandvoices.com/courttney-cooper/.

The Books by the Banks festival is schedule for Saturday, October 20, 10am-5pm in the Duke Energy Center.

ProQuest Downtime on August 18

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Update on our August 18 product downtime
Dear Valued Customer:

To maintain the currency and security of ProQuest products, we are performing maintenance on many ProQuest products beginning on August 18, 2018 U.S. Eastern Time. During the maintenance window, the following products will be temporarily unavailable.

Books products: Saturday, August 18 at 12 p.m. U.S. Eastern Time. Maintenance will conclude within 5 hours.

  • Ebook Central

All other products: Saturday, August 18 at 10 p.m. U.S. Eastern Time. Maintenance will conclude within 8 hours.

Research databases

  • ProQuest Platform (search.proquest.com)
  • ProQuest Congressional (search.proquest.com/congressional, congressional.proquest.com)
  • Chadwyck-Healey databases (U.S. customers only)
  • ProQuest Dissertations & Theses Open
  • ProQuest Dissertations & Theses OAI Repository

Reference management/Research support tools

  • RefWorks

 

UC ‘Life of the Mind’ Series Accepting Nominations

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Life of the Mind is an annual lecture series featuring interdisciplinary conversations with UC faculty from a variety of disciplines around a one-word theme. The fall lecture, scheduled for 3-5 p.m. Tuesday, Oct. 30, will focus on the theme of “next.”

Life of the Mind lectures feature one faculty member presenting his or her work and expertise in concert with the prescribed theme. The presentation is not simply a recitation of the presenter’s work, but promotes a point of view. A panel of three faculty members responds to and discusses the lecture from diverse perspectives, and a moderator encourages audience engagement.

The Life of the Mind Steering Committee seeks nominations for the featured UC faculty presenter. Each featured UC faculty presenter possesses:

  • Accomplished UC faculty member with national/international reputation.
  • Proven record of scholarship or creative works.
  • Recognized as an expert in their field of study, research or creation of works.
  • Experienced at presenting their work to an audience outside the classroom.
  • Excellent and engaging speaker able to relate to a non-specialist audience.
  • Provocative topic of study/research/creative work.

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UC Libraries’ Mark Konecny is Participating in Summit to Examine Affordable Learning Initiatives

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Mark Konecny, scholarly communications and digital publishing strategist and a member of the OhioLINK Affordable Learning group, is an organizer of the Affordable Learning Summit at the University of Akron on Aug. 1 & 2. This summit is a gathering of Ohio institutions to share how faculty, library staff, instructional designers and administrators are addressing affordable learning initiatives.

In announcing the summit, Mark writes, “A recent Florida Virtual Survey of over 22,000 students found that 66.5% of students did not purchase the required textbook / course materials solely due to cost. Recently, Inside Higher Ed shared how the University of Georgia has saved students 3.2 million in textbook cost since 2013 by utilizing Open Educational Resources (OER). In addition, they found that switching to OER increased the number of A and A-minus grades students received by 5.50 percent and 7.73 percent, respectively. The number of students who withdrew or were awarded D or F grades (known as the DFW rate) fell by 2.68 percent.”

Mark is presenting a round table discussion with Kelly Broughton (Ohio University) on the integration of the library with press services. He is also participating in a panel discussion with Sean Kennedy (Ohio University) on authorship, discussing the following topics: how OER creators can partner with their local university press for assistance, issues with creating OERS, common stumbling points and realistic timetables for authoring.

“We know that not having the required course materials directly impacts student success, and the OhioLINK Affordable Learning Initiative is dedicated to addressing this problem,” said Mark.

To learn more, visit https://uakron.edu/affordablelearning/events/. The summit is being live tweeted with the hashtag #alohiosummit.

Recordkeeping and climate change

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The science and history of climate change is intrinsically tied up with the practice of recordkeeping. In climate change conversations we often talk about “records” as in, “the hottest summer on record” or “a record level of flooding.” But those notable milestone records do not reveal themselves – they are revealed because of bits of data, created through the practice of observational recordkeeping, constituting a baseline that makes notable records possible.

One of the longest running data sets related to climate change are the Mauna Loa observatory records from Hawaii. These measurements, still carried out today, record atmospheric carbon dioxide concentrations, and were begun by Charles Keeling in 1958.  The resulting diagram of the measurements, popularly known as the Keeling curve, shows an unmistakable rise in atmospheric concentration of carbon dioxide since it began. The Keeling curve is one of the most important pieces of documentary evidence in demonstrating the phenomenon of climate change, and human contribution towards creating climate change through increased greenhouse gas emissions.

https://scripps.ucsd.edu/programs/keelingcurve/wp-content/plugins/sio-bluemoon/graphs/mlo_full_record.png

The phenomena of climate change is all around us today. But it took decades of maintaining meticulous observational data records, and unearthing other forms of data through historical climate surrogate or proxy records, for climate change to enter mainstream scientific consciousness, let alone popular culture. Scientists had been discussing climate change in disciplinary publications and conferences since the 1960s. But climate change did not begin to enter mainstream conversation or awareness until the mid-1980s. After 1985, various phrases like climate change, global warming, and greenhouse gases began to appear in popular culture. An example of this can be seen in looking at the Google Books Ngram viewer, which registers phrases that appear in its corpus of 5 million digitized books. Around 1986, a major rise begins to take shape, and it gains major steam through the late 1980s.

So what happened in the mid-80s? Several landmark events. One was the Montreal Protocol, which developed international cooperation in reducing the use of chloroflourocarbons (CFCs), which had contributed to the ozone hole. The awareness and international response to the ozone hole helped the public understand the degree to which human activity could adversely impact the environment. Then in 1988, a NASA scientist named James Hansen appeared before Congress during unusually hot summer weather to give testimony that global climate change was happening due to the use of fossil fuels, and that the United States needed to prepare for it.

The New York Times reported that “Dr. Hansen, who records temperatures from readings at monitoring stations around the world, had previously reported that four of the hottest years on record occurred in the 1980’s. Compared with a 30-year base period from 1950 to 1980, when the global temperature averaged 59 degrees Fahrenheit, the temperature was one-third of a degree higher last year. In the entire century before 1880, global temperature had risen by half a degree, rising in the late 1800’s and early 20th century, then roughly stabilizing for unknown reasons for several decades in the middle of the century.” Until this time climate scientists had been hesitant to call for major public policy changes towards averting climate disaster. Hansen’s examination of over 100 years of weather station records led to his determination that global temperature rise was on enough of an upward trajectory than the alarm bell had to be rung.

Jeremy Berberich joins UC Libraries as the Associate Director of Business Affairs

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Today, Jeremy Berberich joined UC Libraries as the associate director of business affairs.  Jeremy comes to UC from Northern Kentucky University where he was the business officer for the College of Health Professions. He previously served as associate vice president for Knowledge Management at Gateway Community and Technical College and prior to that as a reference librarian and associate director for library and information services at Gateway. Jeremy holds a BA in political science with a minor in economics from the University of Louisville, an MLIS from the University of Kentucky and an MBA from Northern Kentucky University.

Jeremy will be a member of the Dean’s Cabinet and will lead the Business Office and HR operations.

Welcome, Jeremy, to UC Libraries.

Greeks and Romans, Happy Halloween!

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The Classics Library’s Welcoming Host Handing Out The Library Guide.

Excerpt from a dialogue between the slave Tranio and his master Theopropides from Plautus’ comedy Mostellaria, The Haunted House. Theopropides’ son has squandered his father’s fortune and the slave Tranio is trying to divert the father’s attention by asserting that the house is haunted before the money lenders arrive to claim it. 

Tranio

“sed ecce quae illi in somnis mortuos:“ego transmarinus hospes sum Diapontius. hic habito, haec mi dedita est habitatio. nam me Accheruntem recipere Orcus noluit, quia praemature uita careo. per fidem deceptus sum: hospes me hic necauit isque medefodit insepultum clam [ibidem] in hisce aedibus, scelestus, auri causa. nunc tu hinc emigra. scelestae [hae] sunt aedes, impia est habitatio.” quae hic monstra fiunt anno uix possum eloqui” (496-505).

“But look what the dead man said to him in his sleep: “I am a guest from overseas, Diapontius. I live here, this dwelling place has been allotted to me: Orcus did not want to receive me into the Underworld because I lost  my life before my time. I was deceived in violation of the obligations of hospitality: my host murdered me here and he secretly put me underground in this house without due rites, for the sake of gold, the criminal. Now move out from here. This house is under a curse, this dwelling place is defiled.” I could barely tell you in a year what apparitions take place here.”

Theopropides

“guttam haud habeo sanguinis, uiuom me accersunt Accheruntem mortui” (508-509).

“I don’t have a drop of blood! The dead are taking me to the Underworld while I’m still alive!”

The Classics Library’s staff shortage has temporarily been relieved by our most recent hire. Come meet Hecate.

Excerpts from Homer’s Odyssey.

“αὐτὰρ ἐπεὶ ψυχὰς μὲν ἀπεσκέδασ᾿ ἄλλυδις ἄλλῃἁγνὴ Περσεφόνεια γυναικῶν θηλυτεράων, ἦλθε δ᾿ ἐπὶ ψυχὴ Ἀγαμέμνονος Ἀτρεΐδαο ἀχνυμένη· περὶ δ᾿ ἄλλαι ἀγηγέραθ᾿, ὅσσοι ἅμ᾿ αὐτῷ οἴκῳ ἐν Αἰγίσθοιο θάνον καὶ πότμον ἐπέσπον. ἔγνω δ᾿ αἶψ᾿ ἔμ᾿ ἐκεῖνος, ἐπεὶ πίεν αἷμα κελαινόν” (Od. 11. 385-90).

“When then holy Persephone had scattered this way and that the ghosts of the women, there came up the ghost of Agamemnon, son of Atreus, sorrowing, and round about him others were gathered, ghosts of all those who were slain with him in the house of Aegisthus, and met their fate. He knew me instantly, when he had drunk the dark blood.”

“δεδάκρυνται δὲ παρειαί, αἵματι δ᾿ ἐρράδαται τοῖχοι καλαί τε μεσόδμαι· εἰδώλων δὲ πλέον πρόθυρον, πλείη δὲ καὶ αὐλή, ἱεμένων Ἔρεβόσδε ὑπὸ ζόφον· ἠέλιος δὲοὐρανοῦ ἐξαπόλωλε, κακὴ δ᾿ ἐπιδέδρομεν ἀχλύς” (Od. 20. 353-57).

“sprinkled with blood are the walls and the fair panels. And full of ghosts is the porch, full also the court, ghosts hastening down to Erebus beneath the darkness, and the sun has perished out of heaven and an evil mist covers all.”

A recent archaeological find by the UC Classics Department of the skeleton of Roman poet Lucretius, proving that St. Jerome was correct in assigning the cause of the poet’s death to a love potion. Exhibition in the circulation area.

The ghost of Clytemnestra in Aeschylus’ Oresteia (Eumenides) when coming upon the furies fast asleep laments.

“ἐγὼ δ᾿ ὑφ᾿ ὑμῶν ὧδ᾿ ἀπητιμασμένη ἄλλοισιν ἐν νεκροῖσιν, ὧν μὲν ἔκτανον ὄνειδος ἐν φθιτοῖσιν οὐκ ἐκλείπεται, αἰσχρῶς δ᾿ ἀλῶμαι· προὐννέπω δ᾿ ὑμῖν ὅτιἔχω μεγίστην αἰτίαν κείνων ὕπο, παθοῦσα δ᾿ οὕτω δεινὰ πρὸς τῶν φιλτάτων οὐδεὶς ὑπέρ μου δαιμόνων μηνίεται κατασφαγείσης πρὸς χερῶν μητροκτόνων” (95-102).

“I am shunned in dishonor like this among the other dead, thanks to you. I am unceasingly taunted among the shades because of those I killed, and I wander disgraced; and I proclaim to you that I receive the greatest blame from them because, though I have suffered so grievously at the hands of those closest to me, none of the divinities is wrathful on my behalf, slaughtered as I have been by matricidal hands.”

A reference for the few…

Excerpt from a letter (XXVII) to Lucinius Sura by Pliny the Younger.

“Initio, quale ubique, silentium noctis; dein concuti ferrum, vincula moveri. Ille non tollere oculos, non remittere stilum, sed offirmare animum auribusque praetendere. Tum crebrescere fragor, adventare et iam ut in limine, iam ut intra limen audiri. Respicit, videt agnoscitque narratam sibi effigiem.”

“At first there was nothing but the general silence of night; then came the clanking of iron and dragging of chains. He did not look up nor stop writing, but steeled his mind to shut out the sounds. Then the noise grew louder, came nearer, was heard in the doorway, and then inside the room. He looked round, saw and recognized the ghost described to him.”

The Library’s most recent book acquisitions.

Dialogue between the ghost of Tantalus and Menippus from Lucian’s Dialogues of the Dead, illustrating that even in death “life” is a struggle.

ΤΑΝΤΑΛΟΣ

“Τοῦτ᾿ αὐτὸ ἡ κόλασίς ἐστι, τὸ διψῆν τὴν ψυχὴν ὡς σῶμα οὖσαν.”

ΜΕΝΙΠΠΟΣ

“Αλλὰ τοῦτο μὲν οὕτως πιστεύσομεν, ἐπεὶ φῂς κολάζεσθαι τῷ δίψει. τί δ᾿ οὖν σοι τὸ δεινὸν ἔσται; ἢ δέδιας μὴ ἐνδείᾳ τοῦ ποτοῦ ἀποθάνῃς; οὐχ ὁρῶ γὰρ ἄλλον ᾅδην μετὰ τοῦτον ἢ θάνατον ἐντεῦθεν εἰς ἕτερον τόπον.”

ΤΑΝΤΑΛΟΣ

“Ὀρθῶς μὲν λέγεις· καὶ τοῦτο δ᾿ οὖν μέρος τῆς καταδίκης, τὸ ἐπιθυμεῖν πιεῖν μηδὲν δεόμενον.”

Tantalus

“It’s just that that’s my punishment—that my ghost should be thirsty as if it were a body.”

Menippus

“Well, we’ll believe it, since you tell us you’re punished by thirst. But what do you find so terrible in that? Are you afraid of dying for lack of drink? I can’t see another Hades after this one, or a death hereafter taking us elsewhere.”

Tantalus

“You are quite right; but this is part of my sentence—to long to drink when I’ve no need.”

Cerberus as a puppy guarding the Gates of Hades.

HAPPY HALLOWEEN, GREEKS AND ROMANS!

FROM THE STAFF OF THE CLASSICS LIBRARY