bluuebunny/crossref_metadata_2025 huggingface dataset:
تطبيق تعليم النحو لفهم مادة اللغة العربية لطلاب فصل الحادي عشر بالمدرسة العالية الحكومية 10 جومبانج
Authors: Fitrawan Tomi , Arif Setyabudi Muhammad
Published: December 2024

This study investigates the application of Arabic grammar teaching to enhance the understanding of Arabic subjects among 11th-grade students at SMAN 10 Jombang. The research employs a qualitative method with a descriptive-analytical approach, using direct observation, interviews, and documentation for data collection. The results show that the grammar teaching implementation includes objectives, methods, media, and evaluations. The objective is to facilitate students' understanding of Arabic grammar rules. The standard or deductive method, which first presents grammar rules followed by examples, is used. Media such as blackboards, YouTube, learning formats created by the grammar teacher, and projectors are utilized. The advantages of this approach include better comprehension of grammar rules, quick understanding of material, increased vocabulary, and additional enrichment materials to facilitate learning Arabic.
The Role of Insulin Resistance and Pancreatic Beta -Cell Dysfunction in Type Two Diabetes: A Review Article
Authors:   Department of pharmaceutical science, College of Pharmacy, University of Thi-Qar, Thi-Qar, 64001, Iraq, Barzan Maysm
Published: December 2024

Type 2 diabetes is a lifelong disease. It has to do with the way your body metabolizes blood sugar. It’s known as being insulin-resistant – meaning the cells in your body don’t respond well to insulin – and eventually as an insulin deficiency. Nobody knows exactly what causes it, but factors include genetics, obesity, no physical activity, and a junk food diet. symptoms are: increased thirst; frequent urination; extreme fatigue; blurred vision; slow healing of wounds. Most people who have type 2 diabetes find out when they have this blood test done or when they have a test that uses their blood. There is no cure for diabetes but you can control it by changing your lifestyle – eating healthy foods, exercising, and keeping a healthy weight. Oftentimes, though, medicines or insulin injections are needed to help with the disease. Prevention: Maintaining a healthy weight, eating a balanced diet rich in whole foods, engaging in regular physical activity, Avoiding smoking and excessive alcohol consumption. Type 2 diabetes is a manageable condition, and early intervention can significantly improve outcomes and quality of life.
Gender Differences in Drug Using Behavior for the Drug Offenders
Authors: Yang Shu-Lung , Tzeng Shu-Ping , Suen Mein-Woei , Hsu Chun-Lung
Published: December 2024

Research on gender differences in substance abuse is prominent. This study surveyed 600 male drug offenders in treatment centers and 585 female offenders in the women's prisons in Taiwan in 2022. It aims to examine gender differences in drug use behavior, including characteristics, motives, multiple drug use, and mental health conditions among Category 1 and 2 drug offenders.
The results indicate that males exhibit a more favorable attitude towards drug use, while females demonstrate greater awareness of its adverse effects. Regarding motives, women are often influenced by others, while men tend to use drugs to cope with stress or seek sensations. Furthermore, peers and friends have a stronger impact on females' drug behavior compared to males. Female drug offenders also engage more in drug trafficking prior to imprisonment. Additionally, male users display more pronounced emotional responses and heightened emotional reactions to drug use.
The study proposes that correctional institutions could aid female drug users in fostering interpersonal skills and reinforcing their values to mitigate negative influences from intimate partners. Additionally, strategies to enhance coping skills, manage drug expectations, and encourage emotional expression are crucial for male drug users. Further implications of the study are elaborated upon.
Head Teachers' Perspectives and Implementation of Green Leadership in Pakistani Secondary Schools
Authors: Dr. Tanzeela Urooj  , Dr. Farrukh Kamran  , Dr. Quratulain  , Dr. Muhammad Jamil
Published: December 2024

This qualitative study was conducted to determine how secondary school head teachers in Punjab Pakistan perceive and carry out green leadership practices. Fifteen head teachers from secondary schools in a district of Punjab were selected using purposive sampling and data was collected through semi-structured interviews. For data analysis, thematic analysis was used with the facilitation of NVivo 15. Four main themes were explored: conceptual understanding of green leadership, implementation strategies and practices, challenges and resource constraints, and motivational and cultural influences. The findings revealed the multiplicity of green leadership, ranging from mere environmentally friendly actions to complete leadership tactics. Implementation strategies encouraged collaborative approaches and engaging stakeholders, while participants discussed curricular and co-curricular activities. Financial constraints, limited infrastructure, and varying support by the stakeholders were identified as major implementation challenges, and religious and cultural values were identified as important motivators of environmental initiatives. Despite these constraints, head teachers developed innovative ways of finding local solutions and quite often, cultural and religious values were mobilized to reinforce environmental initiatives. The findings disseminate knowledge of green leadership implementation in the context of developing countries’ educational sectors and yield evidence-based suggestions for Pakistan’s policymakers and educational administrators focusing on the importance of structured professional development and organized resource support.
ASSESSING THE IMPACT OF GEOPOLITICAL RISKS AND ECONOMIC GROWTH ON TOURISM IN ADVANCED COUNTRIES
Authors: Savaş Yunus
Published: December 2024

The exploration of tourism and its determinants constitutes a well-established domain within research. However, in recent years, the significance of geopolitical risks as a crucial determinant of tourism has gained increasing attention. This study employs a comprehensive analytical framework, incorporating the Kao and Westerlund co-integration test, the panel autoregressive distributed lag (ARDL) model, and Dumitrescu Hurlin (2012) panel causality tests. The analysis focuses on discerning the impact of geopolitical risks and economic growth on tourism receipts across advanced countries, spanning the period from 1996 to 2018. The application of Kao and Westerlund co-integration tests reveals evidence of co-integration among the examined variables. The ARDL model results indicate that geopolitical risks and economic growth are key long-term drivers of tourism receipts: a 1% increase in geopolitical risk raises receipts by about 0.13%, while a 1% GDP increase boosts them by 3.23%. These findings highlight the sustained nature of their influence on tourism receipts over an extended temporal horizon.
The Effectiveness of Constructed Wetlands in Managing Coal Mining Wastewater
Authors: Abdullah Deden Disa , Hamdan Alifal
Published: December 2024

Mining activities, especially coal mining, produce wastewater containing heavy metals such as manganese and iron, which can degrade water quality and harm ecosystems. Effective wastewater management is crucial to meet environmental quality standards and reduce ecological risks. This research aims to evaluate the effectiveness of constructed wetlands in treating coal mine wastewater by assessing critical water quality parameters such as pH, Suspended Solids (TSS), Total Iron (Fe), and Total Manganese (Mn). The research uses a descriptive method involving field sampling and laboratory analysis. Water samples were collected from settling pond BB-18 PPA-BA, both before and after the installation of constructed wetlands. The parameters tested include pH, TSS, Total Iron, and Total Manganese, following standard environmental testing protocols. The implementation of constructed wetlands significantly improved water quality. The measured values after treatment were pH 6.90, TSS 18.20 mg/L, Total Iron 0.31 mg/L, and Total Manganese 2.75 mg/L, all within permissible environmental quality standards. Constructed wetlands effectively reduce pollutants in coal mine wastewater, enabling compliance with environmental quality standards. This approach combines active and passive treatment methods, providing a sustainable and cost-effective wastewater management solution for coal mining operations.
Toma y envío de muestras para laboratorio en bovinos, ovinos y equinos
Authors: Carrillo Álvarez Israel Salomón , Rodrigo Espinoza Jorge , Ortuño Barba Carlos Luis , Loja Pacho Jaime Santiago
Published: December 2024

La toma y envío de muestras para laboratorio en animales como bovinos, ovinos y equinos es fundamental para el diagnóstico preciso de enfermedades, y evaluar la salud animal. El manejo adecuado de muestras de sangre entera es primordial para mantener la integridad de la muestra, y resultados serológicos precisos, permitiendo así un diagnóstico definitivo y tratamiento adecuado. Adicionalmente, contar con protocolos de bioseguridad idóneos previene la incidencia de enfermedades zoonóticas entre otras consecuencias negativas debido a malas prácticas de manejo. Por otro lado, es necesario identificar adecuadamente distintos sitios anatómicos específicos para la obtención de muestras de sangre en diferentes especies, como la vena yugular en equinos u ovinos, y la vena coccígea en bovinos. El estudio destaca la importancia de identificar adecuadamente las muestras para asegurar su trazabilidad, además de la preservación correcta de las mismas, mediante refrigeración o congelación, dependiendo del análisis requerido. De igual manera, se aborda la recolección y su envío adecuado a los laboratorios para análisis microbiológicos y serológicos de otros tipos de muestras como: heces, leche, y contenido ruminal. La recolección debe seguir técnicas específicas según la especie y tipo de muestra: punción en vena yugular, coccígea, mamaria, o arteria femoral para sangre; hisopos para cavidad nasal, conjuntival y rectal; y recolección de leche, heces, y contenido ruminal. En animales muertos, la necropsia permite extraer órganos para análisis, por ello es necesario utilizar equipos adecuados para realizar la recolección.
Comparative segmental evaluation of molecular features of colonic mucosa in villous adenomas
Authors: Korotkevich A. G. , Titov S. E. , Zhilina N. M. , Demenkov P. S. , Veryaskina Y. A. , Bondarev O. I.
Published: December 2024

Aim. This study aims to determine the frequency of solitary villous adenomas by colon segment and to compare the molecular genetic features of villous adenomas with the mucosa of the indexed segment and between different colon segments, as well as to consider the characteristics of unchanged mucosa of similar colon segments.

Methods. A continuous cross-sectional retrospective study of 3,086 colonoscopy results was performed. In the study, 347 cellular specimens were analysed, including 109 villous adenomas, 101 index segment mucosa samples and 137 normal mucosa samples. Detection of miRNAs and mRNAs was conducted using real-time PCR. Somatic mutations were identified with allele-specific PCR and a hydrolysable probe.

Results. The overall frequency of villous adenomas in the structure of all detected epithelial neoplasms was 3%. The frequency of villous adenomas was predominant in the sigmoid colon, while in other segments of the colon their frequency did not differ significantly. The frequency of severe dysplasia was associated with the adenoma diameter. Gene mutations similar to changes in villous adenomas were detected in the mucosa of index segments in the rectum, sigmoid colon and descending colon. Evaluation of the relative expression of 9 miRNAs and 9 protein-coding genes associated with the development of CRC in the mucosa of index segments and similar mucosal segments without adenomas did not reveal significant differences. The medians of relative expression levels of the most relevant markers – NOX1, LGR5, S4A12, TIMP, Ki-67, and TERT genes, as well as miRNA-135b, -20a, -21, -31, and -34a – were compared between different colon sections.

Conclusion. The results suggest that inspecting and biopsying unchanged mucosa, even within the index segment, does not provide insight into the risk of developing villous adenoma.
Aspects of closure of the bronchopleural fistula against the background of pleural empyema
Authors: Nikulin A. V. , Romanikhin A. I. , Gandybina E. G. , Petrovskaya A. A. , Potalova A. R. , Abdullah Y. , Uspenskiy M. S. , Khorobrykh T. V.
Published: December 2024

Aim. This study aims to examine international experience in the treatment of patients with pleural empyema and bronchopleural fistula and compare it with the authors’ findings.

Methods. A systematic search of the literature spanning the past 25 years was conducted using databases such as RSCI, PubMed, and Cochrane, aiming to facilitate studies on the clinical outcomes and pathophysiological mechanisms underlying the formation of bronchopleural fistulas in the context of pleural empyema, as well as on methods for closing such fistulas. The authors present the findings from a cohort study, both prospective and retrospective, involving 136 patients treated for pleural empyema, complicated by bronchopleural fistula, at the Davydovsky State Clinical Hospital № 23.

Results. The methods of treating bronchopleural fistulas can be divided into two groups. The first group involves closing the fistula opening (suturing of the bronchial stump, reamputation and bronchial occlusion). The second group includes operations aimed at replacing the volume of the residual cavity with well-supplied tissues (such as the large omentum and muscles) or reducing the volume of the pleural cavity (thoracoplasty). In the vast majority of cases, the literature describesisolated instances of bronchopleural fistula closure using fibrin glue. According to the authors’ own experience, the effectiveness of treatment with fibrin glue was 100 %, compared to 80.3 % with bronchoblocking.

Conclusion. Improving treatment methods for patients with pleural empyema complicated by bronchopleural fistula, using autologous fibrin glue as a biological stimulator of tissue repair – especially in patients who have had COVID-19-associated pneumonia – is a promising area that warrants further multicenter research.
Awesome People: Andrew Warner
Authors: Apodaca Richard L.
Published: December 2024

Ever since Warren DeLano died, something has been bothering me: I never told him how much I valued what he was doing. What an inspiration he was to me for his energy and vision. How gutsy I thought he was to go against conventional wisdom with actions. How I wanted to emulate his success in business. There’s no excuse for this. And there are others besides Warren who I’m benefiting from - many of whom I don’t know.
Yet Another Free Chemistry Database: Pherobase
Authors: Apodaca Richard L.
Published: December 2024

The creation of free chemical databases continues unabated. Today’s entry is Pherobase, a service dedicated to documenting the relationship between chemical structures and the insect world. Users can search Pherobase by text, or browse a large number of precompiled categories: alphabetical by genus; alphabetical by species; and compounds by genus or species.
Substructure Search From Scratch in Java Part 1 - The Atom Mapping Problem
Authors: Apodaca Richard L.
Published: December 2024

One of the most important capabilities in cheminformatics is mapping the atoms of a

query structure

onto the atoms of a

target structure

. Although useful in itself, the main value of atom mapping comes from the software that gets built on top of it: exact structure comparators, substructure search systems, and query atom/bond search systems such as SMARTS.
Pinpoint Performance Problems with Google Speed Tracer
Authors: Apodaca Richard L.
Published: December 2024

Google Chrome just keeps getting better.
Startup School 2008 at Stanford
Authors: Apodaca Richard L.
Published: December 2024

Startup School is set to take place again this year on April 19th at Stanford University. Having gone last year, I can say it was well worth it. The one day event was a great chance to meet people with all levels of experience in starting companies. The speakers were amazing.
Introducing Balsa
Authors: Apodaca Richard L.
Published: December 2024

When molecular structures are encoded and decoded as short strings, SMILES is more likely than not to be used. In the 34 years since Weininger’s landmark publication, SMILES has been widely adopted by both software vendors and database maintainers. But despite its crucial importance to the fields of both chemistry and cheminformatics, SMILES remains underspecified. This article outlines problem and describes a solution.
Building ChemWriter 2 - Pivotal Tracker for Project Management
Authors: Apodaca Richard L.
Published: December 2024

If you’re involved a software project of any scale, you face the problem of collecting and acting on the numerous bugs, chores, and feature requests relating to it - and doing so in a way that promotes team collaboration. You also face the problem of estimating completion time for various phases of the project. I have to admit that my solutions to these problems have been pretty pathetic in the past: PostIts, crude databases, and the like.
Building a Technology Company the Old-Fashioned Way
Authors: Apodaca Richard L.
Published: December 2024

What’s the secret to making money on the Web? David Heinemeier Hansson’s talk at Startup School 2008 offers a much-needed, but all too easy to ignore, dose of reality. Although some of his comments aren’t nearly as funny out of context, this presentation is well worth the time for anyone serious about building a solid technology business.
From IUPAC Name to Molecular Formula with Ruby CDK
Authors: Apodaca Richard L.
Published: December 2024

Recently, a question was raised on the Yahoo cheminf group list regarding the conversion of IUPAC names into molecular formulas. This can be done quickly with Ruby CDK, as this article will show. Prerequisites This tutorial requires Ruby CDK, which in turn requires Ruby Java Bridge (RJB). A recent Depth-First article described the minimal system configuration required to run RJB on Linux. Another article showed how to install RJB on Windows.
A Workbench for Machine Learning in Chemistry
Authors: Apodaca Richard L.
Published: December 2024

Machine learning has made major inroads into molecular property prediction over the last few years. But with the deluge of techniques and tools comes an increased need to recast what works well into a form usable by non-experts. DeepChem is a toolchain designed to do just that. This article presents a short, simple code example demonstrating how to use DeepChem to train and use a deep convolutional network to predict aqueous solubility.
A Minimal Molecule API
Authors: Apodaca Richard L.
Published: December 2024

Application Programming Interfaces (APIs) are borne of conflicting demands. On the one hand, clients want an API with a lot of features. On the other hand, too many features can lead to bloat and its malevolent cousins: poor performance; brittleness; and steep learning curves. Good APIs strive for the middle ground, offering just enough functionality to solve important problems, while leaving niche features to extensions.
Choose Java for Speed
Authors: Apodaca Richard L.
Published: December 2024

O’Boyle and Hutchison offer some interesting comparisons between Open Source cheminformatics toolkits in a recent

Chemistry Central

article. One of them is contained in the table above, in which the Java cheminformatics library CDK outperforms both the natively-compiled libraries Open Babel and RDKit.
Everything Old is New Again - Wiswesser Line Notation (WLN)
Authors: Apodaca Richard L.
Published: December 2024

Sometimes, searching through the attic of scientific ideas turns up unexpected treasures. Like old clothing styles that suddenly become fashionable again, the passage of time has a way of making old ideas relevant by supplying new context. Those ideas that once enjoyed widespread popularity followed by complete obscurity are especially interesting. This article talks about one of them and why it may matter again.
Python Extensions in Pure Rust with PyO3
Authors: Apodaca Richard L.
Published: December 2024

The previous article in this series described a low-level, manual approach to building Python packages from Rust code. Although effective, the procedure involves writing highly repetitive code blocks in both languages. Fortunately, such repetition isn’t necessary. This article picks up where the last one left off by showing one way to automate the generation of Python packages from Rust libraries.
Fast Substructure Search Using Open Source Tools Part 5 - Relating Molecules to Fingerprints with SQL
Authors: Apodaca Richard L.
Published: December 2024

A molecular fingerprint is a special kind of hash function that can reproducibly place any molecule, known or unknown, into one of a large but finite set of groups. Each molecule will be associated with exactly one fingerprint, but each fingerprint can be associated with multiple molecules. In other words, there exists a one-to-many relationship between fingerprints and molecules.
The SDfile Format
Authors: Apodaca Richard L.
Published: December 2024

Chemical datasets often need to be exchanged with high fidelity. A number of file formats enabling such exchange can be found in the wild but the most common by far is the structure-data file (SDfile, aka “SD File,” “SD file,” or “SDF”). Although the format appears simple on the surface, there are some subtleties to consider. This article takes a closer look at the de facto standard for information exchange in cheminformatics.
Cheminformatics in Korean: An Example of Scientific Self-Organization
Authors: Apodaca Richard L.
Published: December 2024

Hanjo Kim of the Bioinformatics & Molecular Design Research Center (BMDRC) in Seoul, South Korea writes in to tell about his Korean-language cheminformatics blog Agile2Robust. Some of his articles, such as this one on PubChem have been translated from Depth-First; others are based on Depth-First articles. This completes a circle.
The Manic Depressive Chemistry Jobs Market: A 24-Year Perspective
Authors: Apodaca Richard L.
Published: December 2024

This year’s Employment Outlook by C&EN states what by now has become perfectly obvious to every chemist - the job market stinks. As if that weren’t enough, the story Barely Hanging On stands as probably the most pessimistic piece the magazine has published in the last few decades.
Depth-First Article to Appear in Science Blogging Anthology
Authors: Apodaca Richard L.
Published: December 2024

A recent Depth-First article titled “SMILES and Aromaticity: Broken?” has been selected to appear in the science blogging anthology “The Open Laboratory 2007.” This article, along with the 51 other winning entries, will be published as a book that can be purchased from Amazon.com. The book, the second in a series, is aimed at promoting the 2008 North Carolina Science Blogging Conference to be held on January 19, 2008.
Anatomy of a Cheminformatics Web Application: Beautifying Depict
Authors: Apodaca Richard L.
Published: December 2024

A recent article outlined the steps for building a Rails Web application that renders SMILES strings as 2-D molecular images. Although this application, Depict, performed its stated purpose, it was neither much to look at nor as easy to use as it could be. In this tutorial, we’ll give Depict a face-lift and make it more user-friendly.
Hacking PubChem: Query by SMILES
Authors: Apodaca Richard L.
Published: December 2024

Recently, I showed how a simple PubChem API could be built from a few lines of Ruby code. The API we created could retrieve a molfile and a 2-D molecular rendering given a PubChem compound ID (CID). In this tutorial, we’ll see how a SMILES query mechanism can be added to the API, enabling CIDs to be retrieved from any valid SMILES string.
Innovation: What Thinking Outside the Box Actually Means
Authors: Apodaca Richard L.
Published: December 2024

The C&EN blog covers a recent innovation symposium. I generally find high-level discussions about innovation to be not terribly useful because they always seem to skirt the central issue, which I posted as a comment: “You’ll know you’re being innovative if you feel uncomfortable.” That’s the best advice on the subject of innovation I ever got.
Running InChI Anywhere with WebAssembly
Authors: Apodaca Richard L.
Published: December 2024

At the recent NIH Virtual Workshop on InChI, I gave a talk titled

Running InChI Anywhere with WebAssembly

. This article expands some of the major points and answers a couple of questions I got. WebAssembly is a Big Deal Although it’s flown under the radar for years, WebAssembly (aka Wasm) is a big deal.
Game Mechanics in Science: You're Soaking in Them
Authors: Apodaca Richard L.
Published: December 2024

[Flash Content Scrubbed] During a recent talk at the Spring 2010 American Chemical Society Meeting, I spoke about Chempedia and Chempedia Lab, and what makes them unique among chemical information systems. One aspect that seemed to get a lot of interest was the idea that the successful scientific information systems of the future would be designed around compelling game mechanics. Game what?
Don't Let the Sideshow Distract You: H.R. 6845 and What Comes After
Authors: Apodaca Richard L.
Published: December 2024

The next salvo in the ongoing battle to decide whether the Federal Government should be in the scientific publishing business has been fired. H.R. 6845 seeks to preempt the recently-passed law (PL 110-161) requiring recipients of NIH funding to deposit copies of their peer-reviewed manuscripts into PubMed Central. The move is hardly surprising. The aim of PL 110-161 was on face value to promote Open Access.
The RESTful Chemical Tracking System Part 2 - Resources
Authors: Apodaca Richard L.
Published: December 2024

Chemical tracking plays a central role in many laboratories today. From enabling remote collaboration via sample management to helping control stockroom costs, the high degree to which chemical tracking intersects with a number of other important lab activities is unmistakable.
Casual Saturdays: Shoulders of Giants
Authors: Apodaca Richard L.
Published: December 2024

Douglas Prasher knows what it takes to be a true scientific pioneer.
Adobe Flash for Cheminformatics - Fast, Scalable, and Attractive 2D Depiction of Chemical Structures with Vector Graphics
Authors: Apodaca Richard L.
Published: December 2024

The previous article in this series discussed the use of vector graphics markup languages for cheminformatics, in particular for the display of 2D chemical structures. Although vector graphics are well-suited for creating responsive and appealing cheminformatics Web applications, the lack of universal native browser support makes both Scalable Vector Graphics (SVG) and its cousin Vector Markup Language (VML) unattractive at this time.
Growing Pains
Authors: Apodaca Richard L.
Published: December 2024

The loss of a parent, especially in childhood, is one of the most traumatic events a person can experience. Not only do children face the loss itself and all of its emotional and material consequences, but the surviving parent must deal with their own grief while trying to raise children. It’s not surprising that all of the research on this topic points to challenges well into adulthood for surviving children.
Sixty-Four Free Chemistry Databases - Five and Counting...
Authors: Apodaca Richard L.
Published: December 2024

Over at Zusammen, the first five installments in a sixty-four part series on free chemistry databases and Web services have been posted: PubChem Sigma-Aldrich Reaction Search Heterocycles Web Edition Electronic Encyclopedia of Reagents for Organic Synthesis CrystalEye Keep those suggestions for new sites coming in!
Sixty-Four Free Chemistry Databases - Twenty and Counting
Authors: Apodaca Richard L.
Published: December 2024

The twentieth installment of the Sixty-Four Free Chemistry Databases series has recently been added.
Shoreline: A Google Closure Project Template
Authors: Apodaca Richard L.
Published: December 2024

Google Closure is a suite of tools for building scalable JavaScript software. I’ve used it in numerous projects with success. Closure’s biggest limitation is complexity. It can take thirty minutes or more just to get a new project set up and debugged. And if you’re new to Closure, that time can stretch into hours or days. My solution is Shoreline, a complete template for Closure projects. With it, you can: Create BDD-style tests using Jasmine.
Building ChemWriter 2 - JavaScript All the Way Down
Authors: Apodaca Richard L.
Published: December 2024

ChemWriter™ is the chemical structure editor for Web applications. It was designed from the ground up with the strengths and limitations of the Web in mind. Times change and at Metamolecular we’ve been busily creating the next major release of ChemWriter. This is no mere revision, but a complete rewrite of ChemWriter - in JavaScript.
ChemRuby First Look
Authors: Apodaca Richard L.
Published: December 2024

Ruby is a dynamic object oriented scripting language. First released in 1995 by a Japanese programmer, it has recently begun to attract a worldwide audience. The use of Ruby in chemical informatics, although currenly rare, can be expected to increase. One especially interesting project is ChemRuby. Although the website is written in Japanese, there is enough English to get a feel for what ChemRuby is all about.
A Molecular Language for Modern Chemistry: FlexMol and Axial Chirality
Authors: Apodaca Richard L.
Published: December 2024

A recent article introduced FlexMol as a molecular language with the unique capability of encoding axial chirality. A previous article showed how E/Z geometrical isomerism is encoded with FlexMol. Using the popular chiral reagent and ligand 1,1’-bi-2-naphthol (BINOL) as an example, this tutorial will illustrate in detail how axial chirality is encoded in FlexMol. Configuration or Conformation?
Benchmarking Iteration from a Rust Trait
Authors: Apodaca Richard L.
Published: December 2024

Iterators are ubiquitous in Rust and mostly just work. Even so, Rust Iterators carry some noteworthy caveats. For an example, consider the case of returning an Iterator from a method defined on a trait. This article describes the problem and offers evidence supporting a practical and ergonomic solution. A Graph Trait Imagine designing a Rust crate for working with graphs. Here I’m referring to the mathematical construct, not a chart.
Hacking CiteULike - Metascripting with Ruby and Session
Authors: Apodaca Richard L.
Published: December 2024

CiteULike lets users easily manage their bibliographies of scholarly works, and in the process discover other users’ papers on related subjects. One of the most powerful features of CiteULike is its ability to convert arbitrary URLs into fully-formatted bibliographical citations. CiteULike manages to do this while largely avoiding the Buggotea Problem in which multiple URLs pointing to the same work are saved.
Writing Aromatic SMILES
Authors: Apodaca Richard L.
Published: December 2024

SMILES is a de facto standard for chemical structure representation. The core language can be picked up quickly, but just below the surface lie some surprisingly complex concepts. One of the most difficult of these is “aromaticity.” A previous article described a comprehensive approach to reading aromatic SMILES. The following article details a method for writing aromatic SMILES.
Molecular Modeling for Average Joes
Authors: Apodaca Richard L.
Published: December 2024

The Chem Blog recently discussed the usability of computational chemistry software as seen through the eyes of a research chemist. A highlight: I’ll freely admit to knowing very little about computational chemistry software (a situation I hope to change). And as a synthetic organic chemist who worked in industry for several years, I tend to agree with the sentiment above. On the other hand, we had people who we paid to do these things for us.
Wanted: A Few Good Chemists
Authors: Apodaca Richard L.
Published: December 2024

At Metamolecular, we’re hard at work developing a new Web-based chemical information service.
Eleven Qualities of The Perfect Line Notation for the Web
Authors: Apodaca Richard L.
Published: December 2024

If you had to design the perfect line notation for the Web, what would it look like? This is hardly an academic exercise given the central role played by line notations in information systems. For a variety of reasons, existing line notations may not be the right match for the Web. This article explores this question and outlines the main qualities needed by a Web-friendly line notation.
What's Up With Chempedia?
Authors: Apodaca Richard L.
Published: December 2024

You may have noticed that Chempedia is now offline, replaced by a proxy page. The service is being radically redesigned in response to feedback from many individuals over the last year or so. The Web has created unprecedented opportunities for rethinking scientific publication; the goal is to use Chempedia as an adaptable resource for advancing this idea.
A Minimal Graph API
Authors: Apodaca Richard L.
Published: December 2024

Graphs are ubiquitous data structures in computing, appearing in domains ranging from networks to logistics to chemistry. Despite these diverse applications, relatively little has been said about the irreducible elements of graph-like behavior. This article introduces a minimal application programming interface (API) for graphs that I’ve developed over the last several years.
Graphs in Rust: An Introduction to Petgraph
Authors: Apodaca Richard L.
Published: December 2024

Graphs are ubiquitous in science and technology. As such, many software projects use graphs in one form or another. Here I discuss Petgraph, a general-purpose graph library written in Rust. The main features of Petgraph are illustrated with short code samples. About Petgraph Started in 2014, Petgraph is Rust’s most popular graph library. According to crates.io, Petgraph has been downloaded over 2.1 million times.
CDK, the Ruby Way
Authors: Apodaca Richard L.
Published: December 2024

Previous articles have discussed how the Chemistry Development Kit (CDK) can interface with Ruby using the Ruby Java Bridge (RJB). However, each of these articles included a repetitive setup in which the CDK jarfile needed to be copied and the CLASSPATH variable needed to be set. In writing, as in programming, repeating yourself is a sure sign that something needs to be refactored.
Build a Rails Cheminformatics Application in Thirty Minutes
Authors: Apodaca Richard L.
Published: December 2024

A recent article highlighted the Web as a new cheminformatics platform. Advocacy is one thing, but a working, open, demo built with modern technologies is far more compelling. In the following tutorial we’ll build a first-generation cheminformatics Web application using the Ruby on Rails framework and 100% Open Source components. We’ll just cover the essentials here - look for future articles to discuss the underlying technology in more detail.
Look Ma, No Applets!
Authors: Apodaca Richard L.
Published: December 2024

The state of the art in structure editors for chemical Web services is Java applets. Although closed editors have long dominated this field, Open Source editors are a possibly viable option. Java applets are great from a developer’s perspective. But applets are avoided by some end users and IT support for their underlying need to install a Java plug-in of some kind and long startup times.
Reading SMILES with MX
Authors: Apodaca Richard L.
Published: December 2024

The latest release of MX, the Java toolkit for cheminformatics, now supports reading a subset of SMILES strings. Although incomplete, full support for this feature is planned within a few releases. To get an idea of how to use the new SMILES reader, we can use interactive JRuby.
Copyright for Chemists: Promoting Reuse through Open Licensing
Authors: Apodaca Richard L.
Published: December 2024

The previous posts in this series introduced copyright as it applies to chemistry research and underscored one of the many issues that can arise when authors of research communications grant publishers exclusive copyright.
Rust and WebAssembly from Scratch: Hello World with Strings
Authors: Apodaca Richard L.
Published: December 2024

Like most successful duos, Rust and WebAssembly (Wasm) complement each other. Rust is a typesafe systems language with modern tooling and high-level features. WebAssembly is a portable compilation target/execution environment for the Web browser and beyond. The combination makes it possible to write fast, stable software that runs anywhere without recompilation. But there’s a catch.
Small Libraries and GitHub: Applet-Fu
Authors: Apodaca Richard L.
Published: December 2024

If you’ve ever needed to deploy Java applets, you may have found the information on best practices scattered, inconsistent, and unreliable. Applet-Fu is a small JavaScript library that makes it easy to deploy applets by taking advantage of Web standards and features already supported by mainstream browsers. More detailed discussion of Applet-Fu is available from the Metamolecular Products Blog and the ChemWriter Best Practices Deployment Page.
Golden Rules for Open Source
Authors: Apodaca Richard L.
Published: December 2024

Greg Beaver has written an interesting set of ten golden rules for running open source projects. Many of these rules apply to running (or working on) anything. My favorite rule is “3. Despite the evidence, it’s probably your fault.” Greg develops the popular Open Source project PEAR, a packaging tool for PHP that looks similar in concept to RubyGems.
PubChem for Newbies
Authors: Apodaca Richard L.
Published: December 2024

PubChem is arguably the most important free repository of information about small molecules on the planet. Although its size is staggering (over 10 million unique compounds), what makes PubChem important is its completely open approach to chemical information.
Ruby CDK for Newbies
Authors: Apodaca Richard L.
Published: December 2024

Scripting languages and cheminformatics can be a highly-effective combination. With their relaxed syntax, compilation-free execution, and interactive testing environments, scripting languages offer fast development iteration cycles. And scripting languages’ support for manipulating libraries written in other languages can be key in today’s heterogeneous cheminformatics software environment.
NIH Hears Publisher Feedback on Open Access Mandate
Authors: Apodaca Richard L.
Published: December 2024

The NIH heard public comments yesterday on its plans for implementing PL 110-161 Section 218, a new law that grants the agency broad powers to intervene in the scientific publication system. Scientific publishers were out in force. According to The Scientist, Jack Ochs of the American Chemical Society (ACS) was first in line to offer comments: A lot is riding on the outcome.
107 Years of Line-Formula Notations (1861-1968)
Authors: Apodaca Richard L.
Published: December 2024

Apparently, advances in chemical line notations have a history of occurring in clusters. Perhaps the development of InChI will spawn a renaissance in the development and use of line notations. Is there room (or need) for multiple line notation languages, each filling a particular niche, or can a universal line notation ever be developed?
Decoding InChIs with Rino
Authors: Apodaca Richard L.
Published: December 2024

InChI identifiers are unique, ASCII-based molecular identifiers well-suited for chemical informatics on the Web. But they are also much more than that. Encoded in every InChI is all of the information needed to reconstruct a valid, machine-readable molecular representation.
ER
Authors: Apodaca Richard L.
Published: December 2024

It’s very disturbing when your body starts doing things it’s never done before. Adolescence, pregnancy, and older age are all times when this happens to us. A little mental preparation goes a long way here, but not everyone is so lucky. How could anyone find themselves in a situation like this and not be at least a little embarrassed? I sure was. But more than shock or embarrassment, I felt an intense need to get some answers — fast.
Open Benchmarks for Cheminformatics
Authors: Apodaca Richard L.
Published: December 2024

Yesterday’s post on cheminformatics benchmarking generated a number of interesting comments, both here and on a similar article posted to Egon Willighagen’s blog. One thing the discussion highlights is the need for a suite of benchmarks specifically aimed at comparing the performance of diverse cheminformatics toolkits under controlled conditions.
Why Web Development is Hard
Authors: Apodaca Richard L.
Published: December 2024

The very thing you’d like most to do as a developer is the thing your users can’t stand.
Twelve Free Chemistry Databases
Authors: Apodaca Richard L.
Published: December 2024

Just two years ago, trying to find free online chemistry databases was an exercise in futility. Now, they’re sprouting up all over the Web like wildflowers after a wet Spring. What follows is a far-from-complete roundup of some of the more interesting places to start your chemical search. PubChem- The granddaddy of all free chemistry databases. Search over 8 million compounds by a variety of criteria.
Class-Free Object-Oriented Programming
Authors: Apodaca Richard L.
Published: December 2024

Back in 1968, Edsger Dijkstra published his well-known “go to statement considered harmful” letter advocating the abolition of the GOTO statement from high-level programming languages: At the time, GOTO was well-regarded and widely-used, as evidence by the controversy surrounding Dijkstra’s letter and the length of time it took languages supporting GOTO, or its use in languages that sill support it, to decline.
Stereochemistry and the V2000 Molfile Format
Authors: Apodaca Richard L.
Published: December 2024

A previous article offered some reasons to adopt the V3000 molfile format. Although there are several, the one that gets the most attention is “enhanced stereochemistry” support. It should come as no surprise that the cost of this enhancement is increased complexity. Fortunately, V3000’s stereochemistry model extends the one used in V2000. Unfortunately, the V2000 stereochemistry model is not exactly simple.
New Cheminformatics Blog: So Much To Do, So Little Time
Authors: Apodaca Richard L.
Published: December 2024

If you’re into cheminformatics and like well-written analysis, Rajarshi Guha’s new blog is well worth reading. Rajarshi is a longtime contributor to the world of open source cheminformatics, including the CDK and Open Babel projects. His interest in the quantitative side of cheminformatics is apparent in recent articles on faster substructure search, faster fingerprinting, and CDK performance.
Software That Just Works
Authors: Apodaca Richard L.
Published: December 2024

My laptop recently died. Depth-First hasn’t been updated lately due in part to the time it’s taken to get a working replacement. For my new system, I wanted to build a desktop from components and run Linux on it, which is the OS my old system was running. Now, anyone who has done this knows that assembling the hardware is actually the easy part.
18 SMILES Problems as Seen through Twitter Polls
Authors: Apodaca Richard L.
Published: December 2024

SMILES is a de facto standard for chemical data exchange. It’s routinely found in public-facing databases, supported by most widely-used cheminformatics toolkits, and for the last few years has even appeared in the context of machine learning. The problem is that the language was never completely specified. The claim that one of chemistry’s most important data formats is incompletely specified may seem extraordinary.
Computational Perception and Recognition of Digitized Molecular Structures
Authors: Apodaca Richard L.
Published: December 2024

Raster images of 2-D molecular structures are everywhere - in books, in journal articles, on photocopies, in notebooks, and most importantly, on the internet (for example, on this page and this one). Although readily interpretable by humans, these renderings are useless to computer indexing systems - unless they can be translated into machine-readable representational schemes such as connection tables.
Making the Case - Flux-2
Authors: Apodaca Richard L.
Published: December 2024

The number of peer-reviewed publications using the Open Source Java library Chemistry Development Kit (CDK) just keeps growing. The latest addition comes by way of a paper by Fechner and Schneider on ligand-based de novo design. In many areas, Open Source software is used not because it’s free, but because it’s perceived as superior to alternatives. How long will it be before this is true in cheminformatics?
Why I Still Don't Use Connotea
Authors: Apodaca Richard L.
Published: December 2024

Like most scientists, I have a collection of hardcopy journal articles. After they sit on my desk for awhile, I sort them into folders. Each folder has a label such as “dihydroxylation”, “olefin metathesis”, or “InChI”. This system is nothing more than a small ontology. It does the job of building a top-level index of my papers, but it’s not nearly as effective as it could be. There are many problems with ontology.
The Best 55 Online Periodic Tables
Authors: Apodaca Richard L.
Published: December 2024

During the last few years, there have been a few occasions when I’ve been at a computer but without immediate access to a periodic table. My standby is Web Elements, a site that seems to have been around forever. I recently happened onto Jorge Goncalves’ Triple Point, which summarizes the best 55 online periodic tables. Although some of the links are broken, there’s plenty to choose from if Web Elements doesn’t do the job.
Cheminformatics Data Pipelining with KNIME - Getting Started
Authors: Apodaca Richard L.
Published: December 2024

Whether you consider visual workflow/data pipelining environments like Pipeline Pilot useful or not, there’s no denying they’re popular. Within the last few years, KNIME has joined Pipeline Pilot as a widely-used visual programming platform. But unlike Pipeline Pilot, KNIME is released under an open source license, which makes it interesting from the perspective of disruptive technology.
JRuby for Cheminformatics - Reading and Writing InChIs Via the Java Native Interface
Authors: Apodaca Richard L.
Published: December 2024

The increased use of the InChI identifier is making the reading and writing of InChIs a standard cheminformatics capability. Recent articles have discussed the advantages of JRuby for cheminformatics. One disadvantage of JRuby is that code written in C can’t be directly used. The presents a potential problem for libraries, such as the InChI toolkit, that are written in C. Fortunately, the solution is simple.
Octet Fundamentals: A Documented System of Atomic Masses
Authors: Apodaca Richard L.
Published: December 2024

The way that atoms, and particularly their masses, are modeled sets the stage for the kinds of problems a cheminformatics environment can solve. Many systems are currently in use, a reflection of the many different ways there are to think about this problem. This article will introduce the atomic mass system used by Octet, which provides atomic mass values and uncertainties cross-referenced to the primary literature.
Brain Surgery or Die in Three Months
Authors: Apodaca Richard L.
Published: December 2024

By the morning of March 24, the evidence pointed to a lemon-sized, cancerous tumor within my brain’s right parietal lobe. Its presence explained my symptoms in the weeks prior to visiting the ER. At the moment I was lying in a bed waiting to be admitted to the hospital. Clearly there was no chance of going home anytime soon. While waiting, still more neurological tests were performed. Squeeze both fingers. Stick out your tongue.