bluuebunny/crossref_metadata_2025 huggingface dataset:
Regulasi Bantuan Sosial di Kota Manado
Authors: Gerungan Carlo Adrin , Koesoemo Adi Tirto , Rompas Deizen Devens
Published: December 2024

Maksud dari jurnal ini yaitu pelaksanaan regulasi penyaluran bantuan sosial di Kota Manado, Indonesia. Kajian ini penting untuk mengetahui penggunaan dana bantuan sosial terhadap peningkatan kesejahteraan masyarakat Manado. Keterlibatan pemerintah dalam meningkatkan taraf kegidupan atau kesejahteraan masyarakat sangat penting karena salah satu tujuan negara mensejahterakan masyarakat. Perlu regulasi yang dapat sehingga penggunaan dan penyaluran bantuan sosial tepat pada sasaran yaitu masyarakat miskin atau yang mengalami bencana alam. Pemerintah sebagai regulator juga sebagai pelaksana penyaluran bantuan sosial harus transparan serta dapat mempertanggungjawabkan kebijakan serta pelaksanaan penyaluran bantuan sosial, dalam bentuk penyiapan prosedur standar operasi, peencanaan dan pelaksanaan. Pada tataran Pemerintah Kota Manado, pelaksanaan bantuan sosial dilakukan melalui beberapa peraturan dan kebijakan tertentu, serta Instansi pemerintah yang diberikan kewenangan dalam mengatur dan melaksanakan penyaluran bantuan sossial.
Analyze Critical Success Factors in Managing Data Silos to Prevent Poor Data Quality with a Case Study Research Approach
Authors: Rahmanqa Alifio , Wibisono Arif , Ananta Ulisa Sitepu Evi
Published: December 2024

In the context of data silo management in the government sector, Critical Success Factors (CSFs) in data quality are becoming increasingly important, especially for government agencies. Government organizations often face specific challenges in managing data silos in a report due to the complexity of their organizational structure and the large amount of report data that needs to be managed. This research aims to identify, analyze, and understand the relationship between Critical Success Factors (CSFs) in data quality to manage data and prevent data silos in organizations or agencies in report generation using work system theory and provide recommendations for developing strategies to improve data quality in reports. Through a qualitative approach, this research will explore the strategies and practices implemented by government agencies in identifying, preventing, and addressing data silos in reports. For the research methodology, it includes internal surveys with interviews of operators in the government agency. The evaluation results are expected to provide a positive contribution to public services, in the management of report data in the digital era, provide improvements in case of anomalies and deficiencies, and provide a deep understanding related to report generation in a relevant organization or agency.
Hubungan Tingkat Stres Terhadap Kejadian Sindrom Dispepsia Fungsional Pada Mahasiswa Preklinik Fakultas Kedokteran Universitas Mataram
Authors: Juwita Baiq Pelangi , Adni Azizatul , Diatmika I Putu , Parwata Wayan Sulaksmana Sandhi
Published: December 2024

Dispepsia fungsional merupakan kumpulan gejala seperti sensasi nyeri di gastroduodenum, rasa terbakar, rasa penuh dan kembung, mual muntah tanpa adanya kerusakan struktural pada pemeriksaan fisik, laboratorium, radiologi, dan endoskopi. Dispepsia dapat disebabkan oleh pola makan, stres, dan pola hidup yang tidak sehat seperti konsumsi alkohol, merokok, dan kurang olahraga. Penelitian ini bertujuan untuk mengetahui hubungan tingkat stres terhadap kejadian sindrom dispepsia fungsional pada mahasiswa pre-klinik Fakultas Kedokteran Universitas Mataram. Penelitian ini menggunakan metode cross-sectional dengan teknik pengambilan sampel simple random sampling. Data dikumpulkan menggunakan kuesioner. Analisis data dilakukan dengan uji chi-square menggunakan SPSS versi 25. Hasil penelitian menunjukkan bahwa terdapat hubungan signifikan antara tingkat stres dan kejadian sindrom dispepsia fungsional (p = 0,023). Responden dengan tingkat stres sedang memiliki frekuensi tertinggi mengalami sindrom dispepsia fungsional dibandingkan tingkat stres ringan atau berat. Kesimpulannya, semakin tinggi tingkat stres, semakin besar risiko terjadinya sindrom dispepsia fungsional pada mahasiswa. Oleh karena itu, disarankan agar mahasiswa meningkatkan manajemen stres, menjaga pola makan yang sehat, dan menerapkan pola hidup yang baik untuk mencegah terjadinya sindrom dispepsia fungsional. Fakultas juga diharapkan menyediakan program pendukung seperti konseling psikologis untuk membantu mahasiswa dalam mengelola stres.
Edukasi Kader Puskesmas dalam Deteksi Dini Penyakit Jantung Koroner
Authors: Purwowiyoto Sidhi Laksono , Stujanna Endin Nokik , Nurusshofa Zahra , Permatasari Tiara , Hayati Siti Lawuny
Published: December 2024

Penyakit Jantung Koroner (PJK) merupakan salah satu spektrum penyakit jantung yang paling umum di dunia, dengan tingkat morbiditas dan mortalitas yang tinggi. Pada tahun 2020, PJK diperkirakan menjadi penyebab utama kematian global, menyumbang 36% dari seluruh kematian, angka ini dua kali lipat dibandingkan kematian akibat kanker. Di Indonesia, PJK (yang termasuk dalam kategori penyakit sistem sirkulasi) tercatat sebagai penyebab utama kematian, dengan angka 26,4%, atau empat kali lebih tinggi dibandingkan kematian akibat kanker yang hanya sebesar 6%. Dengan demikian, sekitar satu dari empat kematian di Indonesia disebabkan oleh PJKKader puskesmas berfungsi sebagai perpanjangan puskesmas dalam menjangkau dan melayani masyarakat di area kerjanya. Berdasarkan permasalahan ini, kegiatan pengabdian masyarakat bertujuan memberikan edukasi kepada kader puskesmas tentang deteksi dini, pencegahan PJK, dan faktor risikonya. Dengan demikian, kader diharapkan dapat mengedukasi masyarakat dan mendorong mereka untuk melakukan deteksi dini serta pencegahan PJK guna mengurangi angka kematian akibat penyakit ini. Setelah pelaksanaan edukasi, terjadi peningkatan pengetahuan kader tentang PJK, yang terlihat dari kenaikan nilai pretest ke post-test sebesar 19,3%.
Heart Failure Caused by Incidentally Discovered Right Atrial Myxoma: A Rare Case Report
Authors: Atikah Rahmatulhusna , Meilus Budi Patria
Published: December 2024

Primary cardiac tumors, though uncommon, play a significant role in medical practice. Cardiac myxoma is the most common benign cardiac tumor, characterized by varying symptoms depending on the location and size of the tumor. We report the case of a 44-year-old woman with complaints of shortness of breath, upper abdominal pain, and leg oedema. Right atrial myxoma was incidentally found after an echocardiography examination, which is an essential tool for detecting and diagnosing cardiac tumors. The patient exhibited clinical improvement with inotropic therapy and antibiotics and was referred for surgical removal of the tumor. Cardiac myxoma surgical procedures generally have a favorable prognosis with a high survival rate. However, postoperative complications such as arrhythmias and infections require close monitoring. Thus, early diagnosis and appropriate management are essential in addressing cardiac myxoma.
The Influence of a Differentiated Approach on Interest and Learning Outcomes in Shot Put
Authors: Agriansya Deni , Rosani Meilia , Imansyah Farizal
Published: December 2024

This research aims to determine the effect of a differentiated approach on interest and learning outcomes in shot put at SMAN 1 Talang Ubi. This research is a type of quantitative research with a quasi-experimental design type The Nonequivalent Control Group Design. The population in this study was class X at SMAN 1 Talang Ubi which consisted of four classes, namely classes X.1, The selection of research subjects used purposive sampling. Data was collected using questionnaires to determine students’ interest in learning and tests to determine learning outcomes in shot put. Data were analyzed using t-test. The results of this research show that there is an influence of the differentiated approach on (1) interest in learning shot put and (2) learning outcomes in shot put.
Changes in uroflowmetry indicators with automatic interference elimination
Authors: Danilov V. V. , Danilov V. V. , Volnykh I. Yu. , Vashchenko V. V. , Radko D. А. , Danilov V. V. , Shalaeva А. K.
Published: December 2024

Aim. The aim of this article is to compare the values of measured (QMAX) and calculated (QMCLC) maximal urine flow and the values of measured (TQ) and calculated (TQCLC) time to reach maximal flow in a large group of individual uroflowgrams during home uroflowmetry.

Materials and Methods. We analysed 29,110 individual uroflowgrams from 719 patients with prostate adenoma, aged 50 to 73 years (mean age, 60.5 ± 8.2 years), collected between 2004 and 2024. Two algorithms were used: determination of QMAX as the maximum value of the calculated flow (function extremum) and calculation of the actual value of the maximum flow after computer processing to eliminate interference and the WAG-effect (QMCLC).

Results. The data showed the following differences between QMAX and QMCLC in the groups: 16.14 % for volumes up to 100 ml; 14.62 % for 100–200 ml; 13.75 % for 200–300 ml; 13.04 % for 300–400 ml; 14.25 % for 400–500 ml; 14.55 % for 500–600 ml; and 12.65 % for 600+ ml. For TQ and TQCLC values, the group differences were as follows: 3.49 % for volumes up to 100 mL; 2.27 % for 100–200 mL; 0.71 % for 200–300 mL; 0.97 % for 300–400 mL; 0.91 % for 400–500 mL; 3.51 % for 500–600 mL; and 1.51 % for 600+ mL.

Conclusion. The study demonstrated a statistically significant difference between the maximum urine flow (QMAX) values obtained during measurement and the maximum urine flow value, after removing interference and the WAG effect (QMCLS) characteristic of any recorded volumes. Therefore, the accuracy of the data obtained may differ depending on the algorithm of uroflowgram processing. No statistically significant difference was found between TQ and TQCLC parameters. The algorithm of uroflowgrams processing used in the Sigma and Urovest uroflowmetry hardware and software system ensures high accuracy in determining maximum flow values; Urovest, in particular, has demonstrated reliability in this regard. The average determined difference between the QMAX and QMCLC values at different volumes of urination is 14.14 %.
The use of atomic force microscopy to predict complications in moderate acute pancreatitis
Authors: Gulikyan G. N. , Pakhomova R. A.
Published: December 2024

Introduction. In response to the ongoing focus of the global surgical community on the challenges of acute pancreatitis, the assessment of peripheral blood erythrocytes is proposed as a diagnostic method.

Aim. This study aims to identify changes in the erythrocyte membrane associated with moderate-severity acute pancreatitis.

Material and methods. To conduct a prospective multicenter study, venous blood was collected from 48 people. The control group included 15 blood samples taken from clinically healthy individuals. In all samples, the erythrocyte membrane was examined by atomic force microscopy (AFM).

Results of the study. Based on AFM results, samples from 33 patients with a diagnosis of moderate-severity acute pancreatitis were divided into two groups: group 1 of 16 individuals with minimal changes in erythrocytes and group 2 of 17 individuals with more pronounced changes. AFM was used to compare erythrocytes from the control group with erythrocytes from the two patient groups with regard to length, width, height, area, and volume of the erythrocyte and, most importantly, the presence of ulcerative lesions of the membrane.

Discussion. The results of AFM revealed obvious changes in the state of the erythrocyte and its membrane, with more pronounced alterations observed in group 2 patients.

Conclusion. Erythrocyte AFM provides insight into the condition of pancreatic cells in acute pancreatitis of moderate severity. The introduction of erythrocyte AFM as a diagnostic test will enable the prediction of disease progression, allowing for timely intervention and adjustments to patient management strategies.
Pathophysiology, diagnostics and treatment of slow-transit constipation: a review
Authors: Garmanova T. N. , Markaryan D. R. , Lukianov A. M. , Kazachenko E. A. , Uhanov P. G. , Bekova Z. M.
Published: December 2024

Introduction. The work is a review article that examines the pathophysiology, diagnostics and treatment options for slow-transit constipation.

Aim. The main goal of this study is to define slow-transit constipation, describe the primary pathophysiological mechanisms involved in its development, identify key aspects of diagnosing the condition, and thoroughly examine the existing treatment methods and their clinical efficacy.

Methods. A systematic search of the literature in electronic databases PubMed, EMBASE and Cochrane covering the past 20 years was conducted. Studies on clinical outcomes and pathophysiological mechanisms of slow-transit constipation were included in this review prepared in accordance with PRISMA guidelines.

Results. It has been established that, despite the widespread use of conservative therapy for idiopathic chronic constipation, its effectiveness in treating slow-transit constipation is low. Conversely, surgical treatment shows high effectiveness in improving symptoms and quality of life. This brings  up the question about making surgical approach the method of preference in treating slow-transit constipation. Yet, aspects related to the frequency of postoperative complications and the selection of the most appropriate surgical approach remain underexplored, leaving the question of the preferred option open for further investigation.

Conclusion. Despite the limited efficacy of conservative therapy for slow-transit constipation, radical surgical treatment shows significant improvement in symptoms and quality of life, requiring further studies to optimise treatment approaches and investigate postoperative complications.
Stepwise hybrid surgical treatment of inguinal-scrotal and recurrent large lumbar hernias with domain loss in an obese patient with diabetes mellitus
Authors: Plotnikov A. F. , Ershov V. V. , Belosludtsev D. N. , Lazarev N. V. , Gut E. Sh.
Published: December 2024

Aim. This article aims to demonstrate the feasibility of stepwise hybrid surgical treatment for large concomitant ventral hernias with domain loss in a patient with severe coexisting pathology, based on a clinical case managed by the authors.

Methods. An analysis was conducted of a stepwise hybrid – laparoscopic and open – surgical treatment in a 63-year-old patient with inguinal-scrotal and recurrent large lumbar hernias with domain loss, complicated by obesity and diabetes mellitus. To assess the risk of compartment syndrome in the patient, computed tomography was performed, revealing a hernia contents volume-to-abdominal cavity ratio index of 28 %.

Results. A stepwise hybrid surgical treatment – a combination of laparoscopy and the open method – was performed with the use of an uncovered mesh endoprosthesis with an interval of six weeks. Taking into account the high risk of incarceration at the first stage, the inguinal-scrotal hernia was corrected. At the second stage, the recurrent lumbar hernia was eliminated with the addition of the laparoscopic method by open excision of the postoperative scar flap. The hernial defect is covered with a mesh located between the peritoneum and the duplication of the muscular-aponeurotic flap. The postoperative period was uneventful. An analysis of recent literature has revealed that the issue of selecting treatment tactics remains unresolved due to the rare occurrence of this condition. Modern approaches to the treatment of lateral abdominal hernias, including minimally invasive methods – laparoscopic, robotic and hybrid – are analysed, with a focus on methods for preventing compartment syndrome. The application of the stepwise hybrid approach used in a positive outcome after 11 months of follow-up.

Conclusion. At the first stage, it is advisable to operate on a hernia with a high risk of incarceration. The main direction in the treatment of this pathology should be the minimisation of surgical trauma and the prevention of compartment syndrome.
Treatment outcomes in patients with median arcuate ligament syndrome
Authors: Vasilchenko M. I. , Erin S. A. , Khusainov I. R. , Ovchinnikova U. R. , Gololobov G. Yu. , Gadlevsky G. S.
Published: December 2024

Aim. This article aims to present the author’s experience with laparoscopic decompression of the celiac trunk in a patient diagnosed with celiac trunk compression syndrome (Dunbar syndrome).

Methods. This article presents a retrospective analysis of the treatment outcomes in eight patients who underwent surgery between January 2020 and December 2023. The diagnosis was established on the basis of complaints, CT angiography and ultrasound. In all patients, the steps of surgical intervention included access to the abdominal cavity, survey laparoscopy and placement of trocars. Afterwards, the lesser omentum was opened to gain access to the base of the legs of the esophageal opening of the diaphragm. Next, the arcuate ligament was isolated with subsequent intersection, as a result of which the contouring of the celiac trunk was determined.

Results. The average operation time was 93.72 minutes, ranging between 60 and 180 minutes; the average blood loss was 36.25 ml. The average hospital stay was 3.25 days. When assessing longterm results, five patients experienced complete recovery, three patients noted a decrease in the intensity and frequency of pain. After surgery, all patients underwent ultrasound scanning of the celiac trunk; expiratory blood flow velocity and PSV in the SN/PSV were within the reference range.

Conclusion. The study found that in most patients with this disease, the clinical presentation is characterised by complaints of nausea, vomiting, weight loss, and pain after eating or physical activity, which aligns with data from the literature. In diagnosing the disease, the methods of computed angiography and ultrasound of the celiac trunk are of greatest clinical importance. The indication for surgical treatment of Dunbar syndrome is the presence of stenosis of the celiac trunk and symptoms of chronic abdominal ischemia. The study results indicate that laparoscopic decompression of the celiac trunk with dissection of the celiac plexus is a safe and effective treatment method.
OBRuby: A Ruby Interface to Open Babel
Authors: Apodaca Richard L.
Published: December 2024

Open Babel is a widely-used Open Source chemical informatics toolkit written in C++. Although originally designed as a molecular language translator, Open Babel also supports SMARTS pattern recognition, molecular fingerprints, molecular superposition, and other features as well. Open Babel currently offers interfaces for two scripting languages: Python and Perl. Recently, Geoff Hutchison and I have been working to add Ruby to that list.
Hacking PubChem - Convert CAS Numbers into PubChem CIDs with Ruby
Authors: Apodaca Richard L.
Published: December 2024

Although the PubChem system has been discussed in numerous recent D-F articles and elsewhere, there’s much more to the story that hasn’t been told. One of the more intriguing things PubChem can do is look up CAS Numbers for free.
Building Chempedia: Social Networking Applied to Chemistry
Authors: Apodaca Richard L.
Published: December 2024

Chempedia is a free online chemical encyclopedia; it’s also a work in progress, the contents of which are being written by numerous volunteers worldwide. A previous article described initial work toward connecting the people behind Chempedia’s content with the compound monographs they’re writing. This article will describe new features that take this idea much further.
Hashing InChIs
Authors: Apodaca Richard L.
Published: December 2024

The InChI team has announced a proposal for a standardized InChI hashing mechanism. This would create a free, fixed-length, alphanumeric molecular identifier. This is an excellent proposal. One of the biggest problems in working with InChIs (and other line notations such as SMILES) is that even medium-sized molecules produce very long identifiers. Another problem is the use of characters that must be escaped in URLs.
The Power of Simple
Authors: Apodaca Richard L.
Published: December 2024

Evan Williams didn’t set out to build Blogger.com - the original product idea for the company he cofounded was an advanced web-based project management tool. Blogger was created on the side as a way for Evan and his cofounder to update their own weblog. The system was eventually made available to the public. Even as the use of this new blogging service took off, Evan remained reluctant to ditch the original project management tool idea.
CouchDB for Chemistry
Authors: Apodaca Richard L.
Published: December 2024

Creating useful data-driven applications for chemists is not an easy job. Data heterogeneity represents one of the stumbling blocks. Chemists create and use so many different kinds of data, from spectra in XY format to raw FIDs to PDFs to chemical structures to in vivo biological results, that deciding the structure of a database up-front, as required by relational databases can be difficult at best.
Collective Intelligence and the Dumbness of Crowds
Authors: Apodaca Richard L.
Published: December 2024

“Web 2.0” has gotten a lot of people thinking about exciting new forms of collaboration made possible through the Internet. Services like Digg, YouTube, Flickr, and Wikipedia, and especially the way they harness the selfish impulses of individuals for the common good, are seen by many as just the start of even better things to come.
Peculiarities of Chemical Information
Authors: Apodaca Richard L.
Published: December 2024

Fugmann goes on to observe some other points that distinguish chemical information from the information of other fields:

It’s Hard for Computers to Deal with Chemical Structures.

The chemical structure may be a universally understandable language for humans, but not for computers. Searching for chemical structures requires much more advanced and computationally intensive technologies than searching for text.
Chempedia.net - Mashing Up PubChem and Wikipedia
Authors: Apodaca Richard L.
Published: December 2024

PubChem and Wikipedia represent two of the largest open repositories of chemical information in the world. And they complement each other very nicely. PubChem contains mainly low-level chemical structure information whereas Wikipedia contains free-text descriptions of chemical compounds in the form of compound monographs. Both services offer permission and access to copy and reuse their contents.
Conversations with James
Authors: Apodaca Richard L.
Published: December 2024

James Gosling, widely credited as the creator of Java, will be at a special session of the San Diego Java Users’ Group on August 8th. Love it or loathe it, Java has changed the direction of software development, and Gosling has been a major force behind it. Based on the record turnout for last month’s presentation by Google on the Google Web Toolkit (GWT), seating will be scarce. You’ll also need to RSVP beforehand.
Casual Saturdays: Wikipedia in 2001
Authors: Apodaca Richard L.
Published: December 2024

Welcome to Wikipedia! We’re writing a complete encyclopedia from scratch, collaboratively. We started work in January 2001. We’ve got over 6,000 pages already. We want to make over 100,000. So, let’s get to work! Write a little (or a lot) about what you know. Read our welcome message here: Welcome, newcomers!
Chemical Informatics Guys Don't Get It
Authors: Apodaca Richard L.
Published: December 2024

During my time as a synthetic organic chemist and later, a medicinal chemist, there were many times when I wondered why certain chemical information tools were built, why they were built the way they were - especially when they hindered my ability to use them, and why others seemed to go unbuilt despite obvious need for them.
Name That Graph Revealed - Crankshaft, JavaScript and the Coming Marketplace Disruption
Authors: Apodaca Richard L.
Published: December 2024

As some of you have guessed already, the graph from yesterday depicted benchmark data on the Chrome browser’s JavaScript engine performance.
RESTful Cheminformatics
Authors: Apodaca Richard L.
Published: December 2024

Names are powerful. For example, if you work in a field that has a well-recognized title, it’s easy to talk to non-experts about what you do. Doctors, lawyers, NASCAR drivers, actors, and airline pilots all fall into this category. If, on the other hand, you’re a medicinal chemist - well, you’ve got your work cut out for you. Names are especially important in software design.
Five Reasons to Start Using JRuby Now
Authors: Apodaca Richard L.
Published: December 2024

JRuby is an implementation of the Ruby programming language on the Java Virtual Machine. Until about six months ago, JRuby was merely a technical curiosity; few seemed interested in using it for ‘serious’ development work. This perception has changed over the last six months, as JRuby’s progress has accelerated. Here, in no particular order, are five reasons to consider using JRuby for your current or next project.
We Don't Need No Stinkin' Copyright
Authors: Apodaca Richard L.
Published: December 2024

I realize that being the U.S. Government has its advantages, but the copyright notice at the bottom of a recent

J. Chem. Inf. Model.

paper caught my attention: As far as I can tell, this article is not part of the ACS AuthorChoice program.
JRuby for Cheminformatics - Parsing IUPAC Nomenclature with OPSIN
Authors: Apodaca Richard L.
Published: December 2024

Recent articles have discussed the use of JRuby for cheminformatics. We’ve seen how to parse SMILES strings, and read or write InChIs. In this article, we’ll see how easy it is to parse IUPAC nomenclature from JRuby using Peter Corbett’s OPSIN library. Installation After installing JRuby, simply download the OPSIN jarfile and copy it to your JRuby lib directory. You’re done.
An Object-Oriented Framework for Molecular Representation: Getting Started with Octet
Authors: Apodaca Richard L.
Published: December 2024

One of the most important considerations when building an application is the choice of framework. As the quote from the Gang of Four implies, there’s much more to frameworks than just a collection of re-usable code.
Knowing-in-action: Bridging the theory-practice divide in global health
Authors: Sadki Reda
Published: December 2024

The gap between theoretical knowledge and practical implementation remains one of the most persistent challenges in global health. This divide manifests in multiple ways: research that fails to address practitioners’ urgent needs, innovations from the field that never inform formal evidence systems, and capacity building approaches that cannot meet the massive scale of learning required.
Just Add Points?
Authors: Apodaca Richard L.
Published: December 2024

I couldn’t help but look at this slide deck and think about my own experiences with introducing game-like elements into the collection and maintenance of scientific information: Chempedia and Chempedia Lab. One of the most valuable lessons from Sebastian Deterding’s presentation is to start with a specific goal, then create an environment around that goal that makes learning and mastery fun. How do Chempedia and Chempedia Lab do on this point?
Rendering Molecules with SVG on the Web
Authors: Apodaca Richard L.
Published: December 2024

Scalable Vector Graphics (SVG) is an XML-based language for encoding graphical content. Unlike raster image formats such as PNG, JPEG, and GIF, SVG images can be scaled to any resolution without pixelation. Given that 2-D structure diagrams are essentially line drawings, SVG seems like a natural fit for this type of representation. SVG also boasts several advanced features that make it an especially intriguing choice.
Modern Approaches to Data Visualization
Authors: Apodaca Richard L.
Published: December 2024

With the ever-increasing volume and heterogeneity of data that we need to cope with, data visualization is a skill that every effective scientist needs to master. Like most essential scientific skills, data visualization is one of those things that is not so much learned in classes, but rather absorbed from one’s surroundings. So if you want to improve your data visualization skills, where can you turn?
Casual Saturdays: A Thousand Years of Darkness
Authors: Apodaca Richard L.
Published: December 2024

[Video Scrubbed]
Understanding the PyMOL User Interface
Authors: Apodaca Richard L.
Published: December 2024

PyMOL is designed a bit differently from other applications, which can take some getting used to. The tutorial gives a high-level overview of the user interface.
Drugable.com: Web Software for Drug Discovery
Authors: Apodaca Richard L.
Published: December 2024

[Flash Content Scrubbed] Drugable.com is an early-stage, NLM-funded collaboration to build a web-based drug discovery platform. Closed beta is expected to begin in March of 2011. If you view the Web as the natural platform for collaboration in drug discovery, Drugable.com and projects like it will no doubt offer a wealth of lessons to learn from.
Hacking PubChem: Entrez Programming Utilities
Authors: Apodaca Richard L.
Published: December 2024

A recent article poses the question of how to balance the rights of owners of open chemical information resources against those of their users, while promoting an innovative environment for third-party developers. Although PubChem was the focus, the discussion could apply to any other chemical information resource.
From the ACS Exposition - Aureus Turns Published Biological Screening Data Into Information
Authors: Apodaca Richard L.
Published: December 2024

The peer-reviewed literature and patents are chock-full of valuable biological screening data. The problem is not finding it; the problem is putting it all together. A company called Aureus Sciences has stepped into this void by offering a product aimed directly at collating and mining published biological screening data.
Temodar, MGMT Methylation, and the Endless Loop of Bad Glioblastoma Treatments
Authors: Apodaca Richard L.
Published: December 2024

In the days following brain surgery to remove a tennis ball-sized glioblastoma, one term I heard a lot was “next-generation sequencing” (NGS). The idea seemed straightforward enough. Drugs and radiation are blunt instruments, but each tumor is genetically unique. NGS would reveal my tumor’s specific vulnerabilities, which would translate into more effective, targeted treatment.
Scientific Blogging - Ignore It and Be Ignored?
Authors: Apodaca Richard L.
Published: December 2024

I continue to be amazed by the number of people I’ve come into contact with who read Depth-First regularly. Many express appreciation for what I’m doing followed quickly by various reasons why they themselves can’t possibly do it. Not just once or twice, mind you, but almost every time. This is amusing to put it mildly.
Google Closure - Synchronize the Closure Library SVN Using a Git Submodule
Authors: Apodaca Richard L.
Published: December 2024

The last post in this series introduced Google Closure, a suite of JavaScript tools for building and maintaining complex JavaScript projects. Whether you’re just starting out with Closure or have been using it awhile, an important problem you’ll have to solve is how to keep your copy of the Closure Library up-to-date with the Google Closure SVN. This article describes one method for doing so using git.
The Forward Pass Has Been Legalized - Will You Use It?
Authors: Apodaca Richard L.
Published: December 2024

I’m normally not one for sports analogies, but this one just seems to fit so well. Somewhere around 2005, science was a low-scoring game of trying to get the most publications into journals nobody had the time or money to read.
3D Molecular Visualization with Avogadro
Authors: Apodaca Richard L.
Published: December 2024

[Flash Content Scrubbed] Marcus Hanwell discusses the main features of Avogadro, which is a finalist in the 2009 SourceForge Community Choice Awards.
Scrum in Under Ten Minutes
Authors: Apodaca Richard L.
Published: December 2024

Scrum is an approach to project management that emphasizes short iterative cycles. Scrum and Scrum-like approaches are used a lot in software development, particularly when combined with other Agile methodologies, but can be applied to any project. There’s a lot of information available about Scrum - almost too much. This short video by Hamid Shojaee may be helpful in understanding the core ideas.
Extending the V3000 Molfile Format with User-Specified Collections
Authors: Apodaca Richard L.
Published: December 2024

Two versions of the widely-used molfile format exist: V2000 and V3000. As noted previously, the V3000 format introduces several capabilities not present in its predecessor. One of them allows the arbitrary grouping and tagging of certain kinds of features. The documentation hints at this grouping and tagging as a V3000 extension mechanism, but how would that work in practice? This article takes a closer look at the question.
Easily Install PyMOL on Mac OSX
Authors: Apodaca Richard L.
Published: December 2024

PyMOL is a very popular 3-D molecular visualization tool. It also happens to be a great bargain. PyMOL is free, as in open source.
Update: Four Free 2-D Structure Editors for Web Applications
Authors: Apodaca Richard L.
Published: December 2024

A previous article discussing the deployment of four free 2D structure editors has been fixed. The sample pages demonstrating how to obtain a molfile from each have also been restored.
ChemCell - Easily Convert Names and CAS Numbers to Chemical Structures in Excel
Authors: Apodaca Richard L.
Published: December 2024

Note: the same functionality described in this article is now available on Google Spreadsheets.

Chemical databases often start as a list of names or Chemical Abstracts Service (CAS) Registry numbers contained in an Excel spreadsheet. But as more and more expectations get placed on these ad hoc datasets, a point inevitably comes when the assignment of chemical structures becomes necessary.
Fighting Spam on the Cheap with CAPTCHA - A Simple Ruby Library for captchas.net
Authors: Apodaca Richard L.
Published: December 2024

A recent article discussed two free services for cheaply integrating CAPTCHAs into Web applications. One of these services, captchas.net, apparently has no publicly-available Ruby library. Given the popularity of Ruby on Rails for building Web applications, and the increasing need for spam protection offered by services such as captchas.net, it seems only logical that such a library should exist.
Why the Web Isn't Ready for Chemistry
Authors: Apodaca Richard L.
Published: December 2024

Wouldn’t it be wonderful if chemical structure searching were as easy as using Google? Draw your molecule, press a button and get the good stuff first. That day may well arrive, but without the creation of some key technologies, the wait will be very long. This article describes an unsuccessful attempt to bring the chemically-aware Web closer to reality. Recently, I introduced a small Web application called InChIMatic.
How to Fail in Science (or Anything Else)
Authors: Apodaca Richard L.
Published: December 2024

What are the most reliable ways to fail in science? Of course, no scientist sets out to fail, but an understanding of that path can lead to a better understanding of the path to success. By way of Seth Godin’s Blog, I came across some interesting rules for failure. Seth’s article cites the above quoted essay.
Casual Saturdays: Wwwwwipeout
Authors: Apodaca Richard L.
Published: December 2024

It’s a fine line between crazy enough and just crazy. The dilemma is that you never know which category you’re in before you start.
Book Review - Practical Prototype and script.aculo.us
Authors: Apodaca Richard L.
Published: December 2024

Technical books generally fall into one of two categories: tutorials, which rely on examples; and references, which use a high-level, architecture-centric perspective. If you prefer tutorials loaded with good examples framed in relevant context, then Andrew Dupont’s

Practical Prototype and script.aculo.us

may be worth reading.
Eolas and jActivating - Working Around a Workaround
Authors: Apodaca Richard L.
Published: December 2024

If you’ve spent any time using Java applets, you may have run across an annoying little “feature” of Internet Explorer 6/7. Before interacting with an applet, it’s outlined in gray and displays the mouseover message “Click to activate and use this control.” This may not seem like much of an inconvenience, but it seems wrong to waste precious time explaining this kind of thing away to hundreds of perplexed users.
Dark Corners of the Molfile Specification - Sgroups and Substructure Abbreviations
Authors: Apodaca Richard L.
Published: December 2024

The molfile specification is chemistry’s de facto standard for the exchange of chemical structures. Tracing its history back to at least 1979, the V2000 Molfile format is now supported in varying degrees by nearly every vendor and product on the market today. Despite its limitations, molfile has stood the test of time remarkably well.
A Comprehensive Guide FlexMol, A Modern Language for Chemical Representation Part 2: Real-World Problems
Authors: Apodaca Richard L.
Published: December 2024

The last installment in this series discussed the limitations in today’s molecular languages and how FlexMol is designed to overcome them. Although these limitations are clearly present theoretically, what’s the practical effect likely to be? For the last two years, a series of articles highlighting specific examples from the current chemical literature have appeared here.
ChemWriter 2: Fall 2010 ACS Lightning Talk Slides and Ideas for Future Sessions
Authors: Apodaca Richard L.
Published: December 2024

Above is my slide deck from a Lightning Talk on ChemWriter that I gave at the Fall 2010 ACS. Lightning what, you ask? Lightning talks are short talks, typically given in rapid succession at a conference. To its credit, the CINF division of ACS introduced this new format for talks at the Fall 2010 meeting. My talk lasted around 6 minutes and I didn’t have to submit an abstract until a few weeks before the meeting.
Hacking PubChem: Direct Access with FTP
Authors: Apodaca Richard L.
Published: December 2024

A previous article in the Hacking PubChem series pointed out that the entire PubChem database can be downloaded via FTP. This article shows how simple tools written in Ruby can be used to efficiently process the massive amount of data on PubChem’s FTP-server. Prerequisites The only software you’ll need for this tutorial is Ruby. Organization of PubChem’s FTP-Server PubChem is a big database.
Using the Typestate Pattern with Rust Traits
Authors: Apodaca Richard L.
Published: December 2024

Changes to the state of a value can set the stage for later errors. Sometimes these errors occur during subsequent method calls. Other times, the method call itself is the source of the error. Good type systems can make it possible to move these kinds of state bugs from run time to compile time. Indeed, the typestate pattern is often cited a solution, especially for Rust.
The Open Access Ecosystem
Authors: Apodaca Richard L.
Published: December 2024

What happens to an article in an Open Access journal that shuts down? Recently, this question was raised on the Blue Obelisk mailing list about an article published in the Internet Journal of Chemistry (IJC). Because the lights now appear to be out for good at IJC, are its articles lost forever? The good news is that by retaining copyright, authors of Open Access articles have the right to copy or reprocess their work in any form they see fit.
CTfile Character Encoding
Authors: Apodaca Richard L.
Published: December 2024

The CTfile family includes the widely-used serialization formats Molfile and SDfile. Users rarely need to consider the many details of these formats because they’re handled by software. But data corruption can result when one utility misreads the output of another. The problem is especially hard to diagnose when the root cause lies close to the base layer.
Web 2.0 and Chemistry
Authors: Apodaca Richard L.
Published: December 2024

Whatever happened to chemistry and the Web? Stu Borman’s article is a wonderful read, if for no other reason than to illustrate what makes technology predictions so tricky. Borman cites these developments, among others, as evidence of the rise of chemistry on the Web circa 1996: An AltaVista search for the word “chemistry” returned 400,000 documents. (Remember AltaVista?
My InChI Runneth Over
Authors: Apodaca Richard L.
Published: December 2024

The only solution to this problem I’ve found is to set the CSS overflow property to “scroll”: InChI=1/C50H70O14/c1-25(24-51)14-28-17-37(52)50(8)41(54-28)19-33-34(61-50)18-32-29(55-33)10-9-12-46(4)42(58-32)23-49(7)40(62-46)21-39-47(5,64-49)13-11-30-44(60-39)26(2)15-31-36(56-30)22-48(6)38(57-31)20-35-45(63-48)27(3)16-43(53)59-35/h9-10,16,24,26,28-42,44-45,52H,1,11-15,17-23H2,2-8H3/b10-9-
Designing the Obvious
Authors: Apodaca Richard L.
Published: December 2024

Designing good user interfaces is difficult work. One of the hardest things about it is what you’re forced to give up: abandoning your hard-won mental map and adopting that of the user; stripping half the product’s features - and then stripping half of what’s left; and fending off featuritis with a big club as the product matures. Everyone knows these things are important, but for some reason we repeat the same mistakes over and over.
Hacking PubChem - Visually Inspect Results for CAS Number and Keyword Searches
Authors: Apodaca Richard L.
Published: December 2024

A recent article described how PubChem could be used to quickly search for CAS numbers. Although useful, the approach is limited in that only an array of PubChem CIDs was returned. What would be really useful would be a simple way to create a report with entries hyperlinked into the PubChem site itself to aid in visual inspection. In this tutorial, we’ll see how an HTML template and a few extra lines of code can do just that.
Making Your 2D Structures Look Good: Firefly, Styles and Stylesheets
Authors: Apodaca Richard L.
Published: December 2024

Chemists can be very discerning when it comes to chemical structure aesthetics. This is not surprising, given the central role played by 2D chemical structures in the day-to-day work of many chemists. For example, consider the Wikipedia Chemistry/Structure drawing workgroup’s ongoing discussion about achieving a consistent look for chemical structures on the online encyclopedia.
More Open Access in the Sciences: Metal-Based Drugs and Hindawi Publishing
Authors: Apodaca Richard L.
Published: December 2024

A recent article discussed chemistry-related journals in the Directory of Open Access Journals (DOAJ). In going through some of my bookmarks, I stumbled on an Open Access journal that DOAJ doesn’t have: Metal-Based Drugs. Unfortunately, the last available issue of Metal-Based Drugs is from 2002. It’s not clear if this journal is defunct or not. The journal’s Author Guidelines link points to the publisher’s general manuscript submission system.
Standardization in Lab Automation: The SiLA Consortium
Authors: Apodaca Richard L.
Published: December 2024

The growing trend toward chemical and biological laboratory automation has great potential to accelerate scientific discovery. But with this trend comes the need for better coordination among devices built by an increasingly large number of players and based on a bewildering array of specifications.
Self-Referential
Authors: Apodaca Richard L.
Published: December 2024

One of the strange things about writing a blog is stumbling on your own work in Google’s search results. In doing some research for a talk, I noticed that Depth-First articles appear at the top of many Google searches. I’m not sure what to make of this, but for what it’s worth, here are some unquoted Google search terms that currently return a Depth-First article in the top-three results:

free chemistry databases

Number two.
Because Mistakes Happen: Giving ChemPhoto Some Poka-yoke
Authors: Apodaca Richard L.
Published: December 2024

One of the difficulties in creating applications that can write to a user’s filesystem is dealing with the real possibility that a simple, honest, garden-variety mistake can result in consequences ranging from the mildly frustrating to the disastrous.
A Molecular Language for Modern Chemistry: FlexMol and Planar-Chiral Metacyclophanes
Authors: Apodaca Richard L.
Published: December 2024

Previous articles have highlighted FlexMol’s ability to represent nearly all forms of molecular chirality, including many that are alien to popular cheminformatics tools. FlexMol provides just a few basic elements and rules for their combination, resulting in a system that is both extensible and systematic.
Hacking DOI - Interconvert Bibliographic References and DOIs with CrossRef and OpenURL
Authors: Apodaca Richard L.
Published: December 2024

Science is in the middle of a transition from print to the internet as the primary medium of communication. This transition, although a boon for many scientists, creates a host of problems for those dealing with scientific information. For example, how would you interconvert a DOI and its corresponding bibliographic reference? A previous Depth-First article discussed a screen-scraping method as one solution.
The Other Vector Graphics Markup Language
Authors: Apodaca Richard L.
Published: December 2024

Scalable Vector Graphics (SVG) is a technology that enables the creation and publication of high quality images that can be scaled to any resolution. SVG is ideally suited for the Web, and all major browsers now support it - except Internet Explorer (IE). This poses a problem: vector graphics are by far superior to raster images for many applications, but the lack of native IE support makes SVG a non-starter for most developers.
3D Molecule Viewer on the iPhone
Authors: Apodaca Richard L.
Published: December 2024

Portable computing platforms like the iPhone may hold a great deal of untapped potential in science. The last five years have witnessed a sharp increase in their graphics and computational capabilities, with the iPhone setting off a new drive for ever more feature-rich and usable devices. In many lab settings, laptop computers are simply too cumbersome to be practical. A handheld device makes much more sense in these situations.
Rethinking Chemistry Publications - Nature Protocols Makes the Experimental Section a First-Class Citizen
Authors: Apodaca Richard L.
Published: December 2024

Experimental procedures are strange beasts. Loathed (at least temporarily) by those who must prepare them yet central to science, the lowly experimental section is mostly forgotten in the daily struggle of publish or perish. Abstracts, discussions, and conclusions will probably be useless 20 years from now, at least in chemistry. In contrast, the experimental section (and the tables based on them) may well live forever.
Open Source Cheminformatics in Python with MX
Authors: Apodaca Richard L.
Published: December 2024

MX is an open source cheminformatics toolkit written in Java. One of the reasons Java was selected as MX’s development platform is the excellent support now available to interface the Java Virtual Machine to a variety of scripting languages. Of the scripting languages used in cheminformatics, Python stands out for its widespread adoption. This article will outline the steps needed to use MX from Python.
Anatomy of a Cheminformatics Web Application: InChIMatic
Authors: Apodaca Richard L.
Published: December 2024

InChI is an open molecular identifier system. Although InChIs obviate the need for a central registration authority, they are complex enough that they must be generated by computer. Currently, a few desktop molecular editors can generate InChI identifiers. But wouldn’t it be more convenient if this capability existed in a simple Web application that could be used from any computer - anywhere?